bioroebe 0.12.24 → 0.13.31

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Files changed (503) hide show
  1. checksums.yaml +4 -4
  2. data/LICENSE.md +7 -8
  3. data/README.md +566 -354
  4. data/bin/all_positions_of_this_nucleotide +1 -1
  5. data/bin/aminoacid_frequencies +1 -1
  6. data/bin/automatically_rename_this_fasta_file +1 -1
  7. data/bin/base_composition +1 -1
  8. data/bin/batch_create_windows_executables +1 -1
  9. data/bin/bioroebe +12 -1
  10. data/bin/bioroebe_cat +7 -0
  11. data/bin/calculate_exponential_growth +7 -0
  12. data/bin/calculate_n50_value +1 -1
  13. data/bin/calculate_the_frequencies_of_this_species +7 -0
  14. data/bin/chunked_display +1 -1
  15. data/bin/codon_frequency +1 -1
  16. data/bin/codon_to_aminoacid +1 -1
  17. data/bin/colourize_this_fasta_sequence +1 -1
  18. data/bin/complementary_dna_strand +1 -1
  19. data/bin/complementary_rna_strand +1 -1
  20. data/bin/consensus_sequence +1 -1
  21. data/bin/dna_to_rna +1 -1
  22. data/bin/downcase_chunked_display +1 -1
  23. data/bin/download_this_pdb +1 -1
  24. data/bin/fasta_index +1 -1
  25. data/bin/fetch_data_from_uniprot +1 -1
  26. data/bin/filter_away_invalid_nucleotides +1 -1
  27. data/bin/find_substring +1 -1
  28. data/bin/input_as_dna +1 -1
  29. data/bin/is_palindrome +1 -1
  30. data/bin/leading_five_prime +1 -1
  31. data/bin/longest_ORF +1 -1
  32. data/bin/longest_substring +1 -1
  33. data/bin/open_reading_frames +1 -1
  34. data/bin/partner_nucleotide +1 -1
  35. data/bin/plain_palindrome +1 -1
  36. data/bin/random_dna_sequence +1 -1
  37. data/bin/random_sequence +1 -1
  38. data/bin/raw_hamming_distance +1 -1
  39. data/bin/return_longest_substring_via_LCS_algorithm +1 -1
  40. data/bin/reverse_sequence +1 -1
  41. data/bin/short_aminoacid_letter_from_long_aminoacid_name +1 -1
  42. data/bin/show_atomic_composition +1 -1
  43. data/bin/show_fasta_header +1 -1
  44. data/bin/show_nucleotide_sequence +1 -1
  45. data/bin/show_this_dna_sequence +1 -1
  46. data/bin/show_time_now +7 -0
  47. data/bin/sort_aminoacid_based_on_its_hydrophobicity +1 -1
  48. data/bin/strict_filter_away_invalid_aminoacids +1 -1
  49. data/{lib/bioroebe/base/reset.rb → bin/three_delimiter} +9 -6
  50. data/bin/three_to_one +1 -1
  51. data/bin/to_rna +1 -1
  52. data/bin/trailing_three_prime +1 -1
  53. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +1 -1
  54. data/bioroebe.gemspec +6 -7
  55. data/doc/README.gen +534 -322
  56. data/doc/blosum/blosum.md +4 -0
  57. data/doc/compatibility/BIO_PHP.md +20 -18
  58. data/doc/compatibility/README.md +2 -3
  59. data/doc/compatibility/emboss.md +5 -3
  60. data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md} +4 -2
  61. data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md} +36 -33
  62. data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md} +3 -3
  63. data/doc/statistics/statistics.md +12 -10
  64. data/doc/todo/bioroebe_GUI_todo.md +6 -1
  65. data/doc/todo/bioroebe_java_todo.md +3 -2
  66. data/doc/todo/bioroebe_todo.md +328 -310
  67. data/doc/{using_biomart.md → using_biomart/using_biomart.md} +7 -3
  68. data/lib/bioroebe/abstract/features.rb +0 -0
  69. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -1
  70. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +3 -1
  71. data/lib/bioroebe/aminoacids/codon_percentage.rb +18 -10
  72. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +5 -2
  73. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +90 -64
  74. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -3
  75. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +2 -2
  76. data/lib/bioroebe/annotations/create_annotation_format.rb +2 -2
  77. data/lib/bioroebe/base/base.rb +101 -6
  78. data/lib/bioroebe/base/base_module/base_module.rb +9 -1
  79. data/lib/bioroebe/base/colours.rb +3 -0
  80. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +80 -44
  81. data/lib/bioroebe/base/commandline_application/README.md +1 -1
  82. data/lib/bioroebe/base/commandline_application/commandline_application.rb +661 -22
  83. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +2 -1
  84. data/lib/bioroebe/base/infer_the_namespace_module/infer_the_namespace_module.rb +37 -0
  85. data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +1 -6
  86. data/lib/bioroebe/base/prototype/prototype.rb +155 -14
  87. data/lib/bioroebe/biomart/attribute.rb +1 -1
  88. data/lib/bioroebe/biomart/biomart.rb +8 -9
  89. data/lib/bioroebe/biomart/server.rb +1 -1
  90. data/lib/bioroebe/blosum/blosum.rb +2 -2
  91. data/lib/bioroebe/calculate/calculate_blosum_score.rb +5 -3
  92. data/lib/bioroebe/calculate/calculate_gc_content.rb +1 -1
  93. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +5 -3
  94. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +2 -10
  95. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +6 -15
  96. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +4 -2
  97. data/lib/bioroebe/cell/cell.rb +3 -2
  98. data/lib/bioroebe/cell/specialized_cells/B_cell.rb +60 -0
  99. data/lib/bioroebe/cell/specialized_cells/Macrophage.rb +60 -0
  100. data/lib/bioroebe/cell/specialized_cells/README.md +5 -0
  101. data/lib/bioroebe/cell/specialized_cells/T_cell.rb +60 -0
  102. data/lib/bioroebe/cleave_and_digest/cleave.rb +3 -1
  103. data/lib/bioroebe/cleave_and_digest/digestion.rb +1 -1
  104. data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml +93 -0
  105. data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml +72 -0
  106. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -2
  107. data/lib/bioroebe/codons/codon_table.rb +10 -2
  108. data/lib/bioroebe/codons/codons.rb +3 -3
  109. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +18 -15
  110. data/lib/bioroebe/codons/determine_optimal_codons.rb +1 -1
  111. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +4 -2
  112. data/lib/bioroebe/codons/show_codon_tables.rb +1 -1
  113. data/lib/bioroebe/codons/show_codon_usage.rb +1 -2
  114. data/lib/bioroebe/codons/show_this_codon_table.rb +2 -2
  115. data/lib/bioroebe/codons/start_codons.rb +7 -3
  116. data/lib/bioroebe/colours/colour_schemes/README.md +1 -1
  117. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +3 -3
  118. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +3 -3
  119. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +4 -3
  120. data/lib/bioroebe/colours/colour_schemes/helix.rb +3 -1
  121. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +3 -1
  122. data/lib/bioroebe/colours/colour_schemes/score.rb +13 -2
  123. data/lib/bioroebe/colours/colour_schemes/strand.rb +3 -1
  124. data/lib/bioroebe/colours/colour_schemes/turn.rb +3 -1
  125. data/lib/bioroebe/colours/colour_schemes/zappo.rb +1 -1
  126. data/lib/bioroebe/{toplevel_methods/colourize_related_methods.rb → colours/colourize_related_code.rb} +1 -3
  127. data/lib/bioroebe/colours/colourize_sequence.rb +3 -1
  128. data/lib/bioroebe/colours/colours.rb +172 -15
  129. data/lib/bioroebe/configuration/configuration.rb +1 -1
  130. data/lib/bioroebe/constants/GUIs.rb +2 -2
  131. data/lib/bioroebe/constants/constants.rb +1349 -0
  132. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +8 -13
  133. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +9 -3
  134. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +11 -10
  135. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +1 -1
  136. data/lib/bioroebe/count/count_at.rb +2 -1
  137. data/lib/bioroebe/databases/download_taxonomy_database.rb +1 -1
  138. data/lib/bioroebe/dotplots/advanced_dotplot.rb +2 -2
  139. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +2 -2
  140. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +2 -2
  141. data/lib/bioroebe/electron_microscopy/flipy.rb +2 -2
  142. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +3 -11
  143. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +6 -6
  144. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +6 -6
  145. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +2 -2
  146. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +1 -1
  147. data/lib/bioroebe/enzymes/restriction_enzyme.rb +1 -1
  148. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +4 -3
  149. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +1 -1
  150. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +4 -3
  151. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +3 -3
  152. data/lib/bioroebe/ext/main.cpp +0 -1
  153. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +3 -3
  154. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +1 -1
  155. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +1 -1
  156. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +8 -14
  157. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -1
  158. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +1 -1
  159. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +1 -1
  160. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +1 -1
  161. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +37 -11
  162. data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +2 -2
  163. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +1 -1
  164. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +5 -13
  165. data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +1 -1
  166. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -1
  167. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +3 -6
  168. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +3 -3
  169. data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +20 -11
  170. data/lib/bioroebe/genome/genome.rb +1 -1
  171. data/lib/bioroebe/genomes/genome_pattern.rb +17 -16
  172. data/lib/bioroebe/genomes/genome_retriever.rb +4 -2
  173. data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +10 -13
  174. data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb +557 -0
  175. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/aminoacid_composition.rb +498 -198
  176. data/lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb +665 -0
  177. data/lib/bioroebe/gui/universal_widgets/blosum_matrix_viewer/blosum_matrix_viewer.rb +329 -0
  178. data/lib/bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +423 -0
  179. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/controller/controller.rb +170 -118
  180. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +277 -215
  181. data/lib/bioroebe/gui/{shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb → universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb} +297 -107
  182. data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb +643 -0
  183. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/format_converter/format_converter.rb +236 -164
  184. data/lib/bioroebe/gui/universal_widgets/gene/gene.rb +278 -0
  185. data/lib/bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb +646 -0
  186. data/lib/bioroebe/gui/{shared_code/levensthein_distance/levensthein_distance_module.rb → universal_widgets/levensthein_distance/levensthein_distance.rb} +313 -88
  187. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/nucleotide_analyser/nucleotide_analyser.rb +281 -189
  188. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/parse_pdb_file/parse_pdb_file.rb +265 -149
  189. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/primer_design_widget/primer_design_widget.rb +337 -263
  190. data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb +408 -0
  191. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/random_sequence/random_sequence.rb +245 -187
  192. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.rb +207 -137
  193. data/lib/bioroebe/gui/universal_widgets/shell/shell.rb +288 -0
  194. data/lib/bioroebe/gui/{gtk3/show_codon_table/misc.rb → universal_widgets/show_codon_table/show_codon_table.rb} +290 -110
  195. data/lib/bioroebe/gui/{shared_code/show_codon_usage/show_codon_usage_module.rb → universal_widgets/show_codon_usage/show_codon_usage.rb} +228 -47
  196. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/sizeseq/sizeseq.rb +151 -69
  197. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/three_to_one/three_to_one.rb +190 -127
  198. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.rb +211 -152
  199. data/lib/bioroebe/images/images.html +953 -1170
  200. data/lib/bioroebe/images/misc/README.md +6 -0
  201. data/lib/bioroebe/images/misc/activation.avif +0 -0
  202. data/lib/bioroebe/images/misc/inhibition.avif +0 -0
  203. data/lib/bioroebe/images/misc/small_virus_logo.avif +0 -0
  204. data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb} +79 -59
  205. data/lib/bioroebe/matplotlib/matplotlib_generator.rb +1 -1
  206. data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +1 -1
  207. data/lib/bioroebe/misc/ruler.rb +5 -5
  208. data/lib/bioroebe/misc/useful_formulas.rb +3 -3
  209. data/lib/bioroebe/ncbi/efetch.rb +1 -2
  210. data/lib/bioroebe/ngs/phred_quality_score_table.rb +3 -3
  211. data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +3 -6
  212. data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +3 -3
  213. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +6 -10
  214. data/lib/bioroebe/nucleotides/{show_nucleotide_sequence.rb → show_nucleotide_sequence/show_nucleotide_sequence.rb} +377 -255
  215. data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +1 -1
  216. data/lib/bioroebe/palindromes/palindrome_finder.rb +1 -1
  217. data/lib/bioroebe/palindromes/palindrome_generator.rb +2 -10
  218. data/lib/bioroebe/parsers/biolang_parser.rb +1 -1
  219. data/lib/bioroebe/parsers/blosum_parser.rb +14 -19
  220. data/lib/bioroebe/parsers/genbank_parser.rb +2 -6
  221. data/lib/bioroebe/parsers/gff.rb +9 -9
  222. data/lib/bioroebe/parsers/parse_embl.rb +2 -6
  223. data/lib/bioroebe/parsers/stride_parser.rb +4 -12
  224. data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +2 -2
  225. data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +6 -3
  226. data/lib/bioroebe/patterns/profile_pattern.rb +2 -2
  227. data/lib/bioroebe/patterns/rgg_scanner.rb +4 -2
  228. data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb +2 -2
  229. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb +2 -3
  230. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb +4 -4
  231. data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb +2 -2
  232. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb +1 -1
  233. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb +3 -3
  234. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb +3 -3
  235. data/lib/bioroebe/project/project.rb +3 -1
  236. data/lib/bioroebe/raw_sequence/README.md +8 -8
  237. data/lib/bioroebe/raw_sequence/raw_sequence.rb +11 -2
  238. data/lib/bioroebe/regexes/regexes.rb +1 -2
  239. data/lib/bioroebe/requires/commandline_application.rb +3 -1
  240. data/lib/bioroebe/requires/require_all_pdb_files.rb +1 -1
  241. data/lib/bioroebe/requires/require_all_taxonomy_files.rb +1 -1
  242. data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +10 -0
  243. data/lib/bioroebe/requires/require_colours.rb +1 -1
  244. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +5 -7
  245. data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +1 -1
  246. data/lib/bioroebe/requires/require_the_constants.rb +2 -14
  247. data/lib/bioroebe/requires/require_yaml.rb +7 -5
  248. data/lib/bioroebe/sequence/alignment.rb +1 -1
  249. data/lib/bioroebe/sequence/dna.rb +4 -2
  250. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +22 -8
  251. data/lib/bioroebe/sequence/protein.rb +2 -2
  252. data/lib/bioroebe/sequence/reverse_complement.rb +3 -3
  253. data/lib/bioroebe/sequence/rna.rb +9 -8
  254. data/lib/bioroebe/sequence/sequence.rb +3 -3
  255. data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +0 -0
  256. data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +0 -0
  257. data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +0 -0
  258. data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -1
  259. data/lib/bioroebe/shell/help/class.rb +68 -19
  260. data/lib/bioroebe/shell/menu.rb +5244 -5322
  261. data/lib/bioroebe/shell/{readline/readline.rb → readline.rb} +1 -3
  262. data/lib/bioroebe/shell/shell.rb +11240 -453
  263. data/lib/bioroebe/siRNA/siRNA.rb +3 -3
  264. data/lib/bioroebe/{gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb → sinatra/sinatra_interface.rb} +28 -19
  265. data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb} +731 -754
  266. data/lib/bioroebe/string_matching/find_longest_substring.rb +2 -10
  267. data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +4 -14
  268. data/lib/bioroebe/string_matching/hamming_distance.rb +11 -10
  269. data/lib/bioroebe/string_matching/levensthein.rb +5 -17
  270. data/lib/bioroebe/string_matching/simple_string_comparer.rb +48 -4
  271. data/lib/bioroebe/string_matching/smith_waterman.rb +11 -6
  272. data/lib/bioroebe/svg/glyph.rb +4 -1
  273. data/lib/bioroebe/svg/mini_feature.rb +1 -1
  274. data/lib/bioroebe/svg/page.rb +18 -7
  275. data/lib/bioroebe/svg/svgee.rb +22 -13
  276. data/lib/bioroebe/svg/track.rb +20 -4
  277. data/lib/bioroebe/taxonomy/chart.rb +2 -2
  278. data/lib/bioroebe/taxonomy/class_methods.rb +5 -6
  279. data/lib/bioroebe/taxonomy/constants.rb +1 -1
  280. data/lib/bioroebe/taxonomy/info/info.rb +1 -1
  281. data/lib/bioroebe/taxonomy/info/is_dna.rb +1 -1
  282. data/lib/bioroebe/taxonomy/interactive.rb +1 -2
  283. data/lib/bioroebe/taxonomy/menu.rb +1 -1
  284. data/lib/bioroebe/taxonomy/node.rb +1 -1
  285. data/lib/bioroebe/taxonomy/parse_fasta.rb +4 -2
  286. data/lib/bioroebe/taxonomy/shared.rb +5 -4
  287. data/lib/bioroebe/taxonomy/taxonomy.rb +2 -4
  288. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +3 -45
  289. data/lib/bioroebe/toplevel_methods/{is_on_roebe.rb → roebe.rb} +1 -11
  290. data/lib/bioroebe/toplevel_methods/taxonomy.rb +6 -12
  291. data/lib/bioroebe/toplevel_methods/toplevel_methods.rb +5568 -0
  292. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +4 -3
  293. data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +2 -2
  294. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +16 -9
  295. data/lib/bioroebe/utility_scripts/compacter/compacter.rb +4 -2
  296. data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb +119 -0
  297. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +11 -9
  298. data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb} +13 -4
  299. data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb} +5 -5
  300. data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb} +5 -5
  301. data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb} +16 -15
  302. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +7 -7
  303. data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +1 -1
  304. data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +2 -0
  305. data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb} +3 -3
  306. data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb} +5 -5
  307. data/lib/bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb +269 -0
  308. data/lib/bioroebe/utility_scripts/find_gene.rb +4 -2
  309. data/lib/bioroebe/utility_scripts/{mirror_repeat.rb → mirror_repeat/mirror_repeat.rb} +5 -5
  310. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +3 -3
  311. data/lib/bioroebe/utility_scripts/{parse_taxonomy.rb → parse_taxonomy/parse_taxonomy.rb} +15 -6
  312. data/lib/bioroebe/utility_scripts/{pathways.rb → pathways/pathways.rb} +4 -3
  313. data/lib/bioroebe/utility_scripts/{permutations.rb → permutations/permutations.rb} +3 -3
  314. data/lib/bioroebe/utility_scripts/punnet/punnet.rb +4 -2
  315. data/lib/bioroebe/utility_scripts/{show_this_dna_sequence.rb → show_this_dna_sequence/show_this_dna_sequence.rb} +1 -1
  316. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +406 -10
  317. data/lib/bioroebe/version/version.rb +2 -2
  318. data/lib/bioroebe/viennarna/rnafold_wrapper.rb +5 -13
  319. data/lib/bioroebe/virus/individual_viruses/README.md +15 -0
  320. data/lib/bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb +40 -0
  321. data/lib/bioroebe/virus/virus.rb +76 -0
  322. data/lib/bioroebe/www/bioroebe.cgi +4 -3
  323. data/lib/bioroebe/www/embeddable_interface.rb +85 -49
  324. data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +6 -6
  325. data/lib/bioroebe/yaml/antisense/antisense.yml +2 -0
  326. data/lib/bioroebe/yaml/blosum/blosum50.yml +6 -0
  327. data/lib/bioroebe/yaml/blosum/blosum90.yml +2 -1
  328. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +2 -2
  329. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  330. data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
  331. data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +7 -6
  332. data/lib/bioroebe/yaml/humans/human_chromosomes.yml +3 -3
  333. data/lib/bioroebe/yaml/mRNA/mRNA.yml +1 -5
  334. data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +1 -0
  335. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +2 -1
  336. data/lib/bioroebe/yaml/promoters/35S.yml +3 -1
  337. data/lib/bioroebe/yaml/proteases/proteases.yml +3 -1
  338. data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -1
  339. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +7 -7
  340. data/spec/testing_toplevel_method_editor.rb +1 -1
  341. data/spec/testing_toplevel_method_verbose.rb +1 -1
  342. data/test/testing_dna_to_rna_conversion.rb +1 -1
  343. metadata +127 -235
  344. data/doc/blosum.md +0 -5
  345. data/lib/bioroebe/base/commandline_application/aminoacids.rb +0 -33
  346. data/lib/bioroebe/base/commandline_application/directory.rb +0 -33
  347. data/lib/bioroebe/base/commandline_application/extract.rb +0 -22
  348. data/lib/bioroebe/base/commandline_application/misc.rb +0 -502
  349. data/lib/bioroebe/base/commandline_application/opn.rb +0 -47
  350. data/lib/bioroebe/base/commandline_application/reset.rb +0 -42
  351. data/lib/bioroebe/base/commandline_application/warnings.rb +0 -36
  352. data/lib/bioroebe/base/commandline_application/write_what_into.rb +0 -29
  353. data/lib/bioroebe/base/initialize.rb +0 -18
  354. data/lib/bioroebe/base/misc.rb +0 -129
  355. data/lib/bioroebe/base/namespace.rb +0 -16
  356. data/lib/bioroebe/base/prototype/e_and_ee.rb +0 -24
  357. data/lib/bioroebe/base/prototype/misc.rb +0 -114
  358. data/lib/bioroebe/base/prototype/mkdir.rb +0 -20
  359. data/lib/bioroebe/base/prototype/reset.rb +0 -36
  360. data/lib/bioroebe/colours/misc_colours.rb +0 -80
  361. data/lib/bioroebe/colours/rev.rb +0 -44
  362. data/lib/bioroebe/colours/sdir.rb +0 -21
  363. data/lib/bioroebe/colours/sfancy.rb +0 -21
  364. data/lib/bioroebe/colours/sfile.rb +0 -21
  365. data/lib/bioroebe/colours/simp.rb +0 -21
  366. data/lib/bioroebe/colours/swarn.rb +0 -29
  367. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +0 -147
  368. data/lib/bioroebe/constants/carriage_return.rb +0 -14
  369. data/lib/bioroebe/constants/codon_tables.rb +0 -77
  370. data/lib/bioroebe/constants/database_constants.rb +0 -107
  371. data/lib/bioroebe/constants/files_and_directories.rb +0 -606
  372. data/lib/bioroebe/constants/misc.rb +0 -209
  373. data/lib/bioroebe/constants/newline.rb +0 -14
  374. data/lib/bioroebe/constants/nucleotides.rb +0 -121
  375. data/lib/bioroebe/constants/regex.rb +0 -28
  376. data/lib/bioroebe/constants/roebe.rb +0 -38
  377. data/lib/bioroebe/constants/row_terminator.rb +0 -16
  378. data/lib/bioroebe/constants/tabulator.rb +0 -14
  379. data/lib/bioroebe/constants/unicode.rb +0 -12
  380. data/lib/bioroebe/constants/urls.rb +0 -50
  381. data/lib/bioroebe/gui/gtk +0 -1
  382. data/lib/bioroebe/gui/gtk3/README.md +0 -2
  383. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +0 -306
  384. data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +0 -29
  385. data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -195
  386. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -105
  387. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -188
  388. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +0 -322
  389. data/lib/bioroebe/gui/gtk3/gene/gene.rb +0 -181
  390. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +0 -383
  391. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +0 -174
  392. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +0 -181
  393. data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +0 -101
  394. data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +0 -145
  395. data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +0 -23
  396. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +0 -165
  397. data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +0 -166
  398. data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -82
  399. data/lib/bioroebe/gui/libui/README.md +0 -4
  400. data/lib/bioroebe/gui/libui/alignment/alignment.rb +0 -116
  401. data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -112
  402. data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -60
  403. data/lib/bioroebe/gui/libui/controller/controller.rb +0 -116
  404. data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +0 -161
  405. data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -76
  406. data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +0 -135
  407. data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +0 -118
  408. data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +0 -115
  409. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +0 -190
  410. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +0 -134
  411. data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +0 -89
  412. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +0 -113
  413. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +0 -102
  414. data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +0 -94
  415. data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +0 -216
  416. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +0 -192
  417. data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +0 -72
  418. data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +0 -206
  419. data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -140
  420. data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +0 -262
  421. data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +0 -243
  422. data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +0 -199
  423. data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +0 -519
  424. data/lib/bioroebe/shell/colours/colours.rb +0 -235
  425. data/lib/bioroebe/shell/help/help.rb +0 -25
  426. data/lib/bioroebe/shell/misc.rb +0 -10227
  427. data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +0 -56
  428. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +0 -722
  429. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +0 -198
  430. data/lib/bioroebe/toplevel_methods/base_composition.rb +0 -121
  431. data/lib/bioroebe/toplevel_methods/blast.rb +0 -153
  432. data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +0 -57
  433. data/lib/bioroebe/toplevel_methods/cat.rb +0 -71
  434. data/lib/bioroebe/toplevel_methods/chunked_display.rb +0 -92
  435. data/lib/bioroebe/toplevel_methods/cliner.rb +0 -81
  436. data/lib/bioroebe/toplevel_methods/complement.rb +0 -58
  437. data/lib/bioroebe/toplevel_methods/convert_global_env.rb +0 -39
  438. data/lib/bioroebe/toplevel_methods/databases.rb +0 -73
  439. data/lib/bioroebe/toplevel_methods/delimiter.rb +0 -19
  440. data/lib/bioroebe/toplevel_methods/digest.rb +0 -81
  441. data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +0 -146
  442. data/lib/bioroebe/toplevel_methods/e.rb +0 -20
  443. data/lib/bioroebe/toplevel_methods/editor.rb +0 -21
  444. data/lib/bioroebe/toplevel_methods/esystem.rb +0 -22
  445. data/lib/bioroebe/toplevel_methods/exponential_growth.rb +0 -74
  446. data/lib/bioroebe/toplevel_methods/extract.rb +0 -56
  447. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +0 -269
  448. data/lib/bioroebe/toplevel_methods/frequencies.rb +0 -99
  449. data/lib/bioroebe/toplevel_methods/hamming_distance.rb +0 -60
  450. data/lib/bioroebe/toplevel_methods/infer.rb +0 -66
  451. data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +0 -101
  452. data/lib/bioroebe/toplevel_methods/levensthein.rb +0 -63
  453. data/lib/bioroebe/toplevel_methods/log_directory.rb +0 -109
  454. data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +0 -55
  455. data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +0 -88
  456. data/lib/bioroebe/toplevel_methods/matches.rb +0 -259
  457. data/lib/bioroebe/toplevel_methods/misc.rb +0 -596
  458. data/lib/bioroebe/toplevel_methods/nucleotides.rb +0 -787
  459. data/lib/bioroebe/toplevel_methods/number_of_clones.rb +0 -63
  460. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +0 -79
  461. data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +0 -236
  462. data/lib/bioroebe/toplevel_methods/opn.rb +0 -34
  463. data/lib/bioroebe/toplevel_methods/palindromes.rb +0 -155
  464. data/lib/bioroebe/toplevel_methods/parse.rb +0 -59
  465. data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +0 -68
  466. data/lib/bioroebe/toplevel_methods/rds.rb +0 -24
  467. data/lib/bioroebe/toplevel_methods/remove.rb +0 -86
  468. data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +0 -35
  469. data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +0 -68
  470. data/lib/bioroebe/toplevel_methods/rna_splicing.rb +0 -73
  471. data/lib/bioroebe/toplevel_methods/rnalfold.rb +0 -69
  472. data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +0 -116
  473. data/lib/bioroebe/toplevel_methods/shuffleseq.rb +0 -37
  474. data/lib/bioroebe/toplevel_methods/statistics.rb +0 -53
  475. data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +0 -62
  476. data/lib/bioroebe/toplevel_methods/three_delimiter.rb +0 -34
  477. data/lib/bioroebe/toplevel_methods/time_and_date.rb +0 -53
  478. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +0 -31
  479. data/lib/bioroebe/toplevel_methods/truncate.rb +0 -48
  480. data/lib/bioroebe/toplevel_methods/url.rb +0 -36
  481. data/lib/bioroebe/toplevel_methods/verbose.rb +0 -59
  482. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -31
  483. data/lib/bioroebe/utility_scripts/showorf/help.rb +0 -33
  484. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +0 -52
  485. data/lib/bioroebe/utility_scripts/showorf/menu.rb +0 -68
  486. data/lib/bioroebe/utility_scripts/showorf/reset.rb +0 -36
  487. data/lib/bioroebe/utility_scripts/showorf/run.rb +0 -152
  488. data/lib/bioroebe/utility_scripts/showorf/show.rb +0 -97
  489. /data/doc/{german_names_for_the_aminoacids.md → german_names_for_the_aminoacids/german_names_for_the_aminoacids.md} +0 -0
  490. /data/doc/{pdb_ATOM_entry.md → pdb_ATOM_entry/pdb_ATOM_entry.md} +0 -0
  491. /data/doc/{resources.md → resources/resources.md} +0 -0
  492. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/customized_dialog.rb +0 -0
  493. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/anti_sense_strand/anti_sense_strand.config +0 -0
  494. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +0 -0
  495. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +0 -0
  496. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/hamming_distance/hamming_distance.config +0 -0
  497. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/levensthein_distance/levensthein_distance.config +0 -0
  498. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/protein_to_DNA/protein_to_DNA.config +0 -0
  499. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.config +0 -0
  500. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.config +0 -0
  501. /data/lib/bioroebe/yaml/{base_composition_of_dna.yml → base_composition_of_dna/base_composition_of_dna.yml} +0 -0
  502. /data/lib/bioroebe/yaml/{nuclear_localization_sequences.yml → nuclear_localization_sequences/nuclear_localization_sequences.yml} +0 -0
  503. /data/lib/bioroebe/yaml/{talens.yml → talens/talens.yml} +0 -0
data/doc/todo/bioroebe_todo.md CHANGED
@@ -1,38 +1,53 @@
1
1
  --------------------------------------------------------------------------------
2
+ add support for
3
+
4
+ class Cell
5
+ class Immunoglobulin
6
+ hmmm
7
+ then add
8
+
9
+ class B_cell
10
+ class T_cell
11
+ class Macrophage
12
+ ^^^^ for testing purposes mostly
13
+ And then perhaps a few more cells. And we need to
14
+ add features to these.
15
+
16
+ --------------------------------------------------------------------------------
17
+ (1) → add support for:
18
+ codon_of? this_aminoacid
19
+ class CodonOfThisAminoacid
20
+ ^^^^ ^^^^^^
21
+ --------------------------------------------------------------------------------
2
22
  (2) → Integrate http://nc2.neb.com/NEBcutter2/cutshow.php?name=ffe1d68e-
3
23
  in particular the visual part.
4
24
  --------------------------------------------------------------------------------
5
- (3) → add support for:
6
- codon_of? this_aminoacid
7
- class CodonOfThisAminoacid
8
- ^^^^
9
- --------------------------------------------------------------------------------
10
- (4) → Bioroebe::RestrictionEnzymes::Statistics.show
25
+ (3) → Bioroebe::RestrictionEnzymes::Statistics.show
11
26
  ^^^ improve these
12
27
  and then add it to the documentation.
13
28
  --------------------------------------------------------------------------------
14
- (5) → use glimmer + nebula for widgets
29
+ (4) → use glimmer + nebula for widgets
15
30
  ^^^
16
31
  improve the nucleotide sequence analyser
17
32
  --------------------------------------------------------------------------------
18
- (6) → add to sinatra: a standalone server to query BAM files (and
33
+ (5) → add to sinatra: a standalone server to query BAM files (and
19
34
  the corresponding reference). The server will return the
20
35
  content of a BAM file in the selected folder when the
21
36
  server is started up. The server used is sintra.
22
37
  --------------------------------------------------------------------------------
23
- (7) → add the possibility to show what the effect of enzymes
38
+ (6) → add the possibility to show what the effect of enzymes
24
39
  are
25
40
  AND inhibitors of enzymes. perhaps bioroebe can be
26
41
  used in system biology one day
27
42
  --------------------------------------------------------------------------------
28
- (8) → Bioroebe::Sequence.new('AGCTTAGCGTACAGCTACGACGTAGTCTGACGA').cut_with? :AluI
43
+ (7) → Bioroebe::Sequence.new('AGCTTAGCGTACAGCTACGACGTAGTCTGACGA').cut_with? :AluI
29
44
  ^^^ support this API and document it too
30
45
  --------------------------------------------------------------------------------
31
- (9) → integrate electrno microscopy slowly and also add documentation
46
+ (8) → integrate electrno microscopy slowly and also add documentation
32
47
  about this AS YOU GO!!!!!
33
48
  ^^^ yup add more of it
34
49
  --------------------------------------------------------------------------------
35
- (10) → Add save session support
50
+ (9) → Add save session support
36
51
  to reload our last activity completely ...
37
52
  hmmm..
38
53
  This has to be well designed...
@@ -47,7 +62,7 @@
47
62
  upon startup of the bioroebe shell.
48
63
  This is in preparation for save-session support.
49
64
  --------------------------------------------------------------------------------
50
- (11) → Lys-Asp-Glu-Leu
65
+ (10) → Lys-Asp-Glu-Leu
51
66
  if i.include?('-') and Bioroebe.is_in_the_three_letter_code?(i)
52
67
  end
53
68
  - Lys-Asp-Glu-Leu-COO-
@@ -59,10 +74,10 @@
59
74
  ^^ yep this is also called KDEL
60
75
  https://en.wikipedia.org/wiki/KDEL_(amino_acid_sequence)
61
76
  --------------------------------------------------------------------------------
62
- (12) → Add "orthologs". this shall show us the top 25 orthologs or
77
+ (11) → Add "orthologs". this shall show us the top 25 orthologs or
63
78
  something. In the bioshell? Hmm. Not sure yet.
64
79
  --------------------------------------------------------------------------------
65
- (13) → clone the functionality of this:
80
+ (12) → clone the functionality of this:
66
81
  http://www.kazusa.or.jp/codon/cgi-bin/countcodon.cgi
67
82
  http://www.kazusa.or.jp/codon/countcodon.html
68
83
  In other words, create a class that can generate such an output.
@@ -72,15 +87,15 @@
72
87
  widget first. And sinatra output too.
73
88
  AND document it as well
74
89
  --------------------------------------------------------------------------------
75
- (14) → SARS genom analyisere in bioroebe
90
+ (13) → SARS genom analyisere in bioroebe
76
91
  eventuell auch graphisch
77
92
  Gibt es neue GUIs die wir kombinieren könnten? Hmmm.
78
93
  --------------------------------------------------------------------------------
79
- (15) → In bioroebe, generate that .ps thingy graphical thing from the
94
+ (14) → In bioroebe, generate that .ps thingy graphical thing from the
80
95
  vienna RNA tutorial. Hmmm.
81
96
  https://www.tbi.univie.ac.at/RNA/tutorial/
82
97
  --------------------------------------------------------------------------------
83
- (16) → get insulin squence frmo NCBI
98
+ (15) → get insulin squence frmo NCBI
84
99
  human
85
100
  then apply trypsin onto it
86
101
  and try it like this:
@@ -92,12 +107,12 @@
92
107
  ^^^ to show it
93
108
  Hmm. Perhaps also auto-download or something.
94
109
  --------------------------------------------------------------------------------
95
- (17) → in bioroebe: UAG?
110
+ (16) → in bioroebe: UAG?
96
111
  ^^^ show all stop codons with that in the bioshell
97
112
  all UAG sequences... hmm. and TAG?
98
113
  Finish that.
99
114
  --------------------------------------------------------------------------------
100
- (18) → The position of a symbol in a string is the total number of
115
+ (17) → The position of a symbol in a string is the total number of
101
116
  symbols found to its left, including itself (e.g., the positions
102
117
  of all occurrences of 'U' in "AUGCUUCAGAAAGGUCUUACG" are 2, 5,
103
118
  6, 15, 17, and 18). The symbol at position i
@@ -105,10 +120,10 @@
105
120
  ^^^ add a solution there, a toplevel API
106
121
  !!!!!
107
122
  --------------------------------------------------------------------------------
108
- (19) → http://bioruby.org/rdoc/Bio/Blast.html
123
+ (18) → http://bioruby.org/rdoc/Bio/Blast.html
109
124
  ^^^ add support for BLAST
110
125
  --------------------------------------------------------------------------------
111
- (20) → add: parse_pdb()
126
+ (19) → add: parse_pdb()
112
127
  With this we shall just show some info, about a given
113
128
  .pdb file at hand.
114
129
  Also make it commandline based too + bioshell variant
@@ -116,55 +131,55 @@
116
131
  Don't forget to document it!!!!!
117
132
  ^^^ and google a bit how others do that
118
133
  --------------------------------------------------------------------------------
119
- (21) → pdb 1a6m
134
+ (20) → pdb 1a6m
120
135
  ^^^ download this when that is used in the bioshell; we also have
121
136
  to use the download directory for this, so make sure that
122
137
  we do.
123
138
  ^^^ And then, also document this clearly.
124
139
  --------------------------------------------------------------------------------
125
- (22) → show_string
140
+ (21) → show_string
126
141
  ^^^ slowly port this ... find out differences
127
142
  then unify into one method. right now we used
128
143
  two or something.
129
144
  --------------------------------------------------------------------------------
130
- (23) → Try to see if we can integrate this into our GUI:
145
+ (22) → Try to see if we can integrate this into our GUI:
131
146
  https://cdn.snapgene.com/assets/7.6.11/assets/images/snapgene/homepage/homepage-hero.png
132
147
  --------------------------------------------------------------------------------
133
- (24) → Scan for leucine zipper!
148
+ (23) → Scan for leucine zipper!
134
149
  This is ~25% implemented. We need to double-check what
135
150
  exactly is a leucine zipper.
136
151
  --------------------------------------------------------------------------------
137
- (25) → Extend the sinatra-interface for the Rosalind task,
152
+ (24) → Extend the sinatra-interface for the Rosalind task,
138
153
  perhaps add a sub-link to show which parts are solved
139
154
  as-is. Hmm. I am not continuing on this though.
140
155
  ^^^^
141
156
  well - make rosalind anew again or something.
142
157
  --------------------------------------------------------------------------------
143
- (26) → Add a blast interface; both via the web-interface, GUI,
158
+ (25) → Add a blast interface; both via the web-interface, GUI,
144
159
  and also from the commandline.
145
160
  --------------------------------------------------------------------------------
146
- (27) → Write a tutorial about primer design.
161
+ (26) → Write a tutorial about primer design.
147
162
  also make sure that the GUI has support for this.
148
163
  --------------------------------------------------------------------------------
149
- (28) → In the documentation examples, show some exampls for how to work
164
+ (27) → In the documentation examples, show some exampls for how to work
150
165
  with different organisms.
151
166
  --------------------------------------------------------------------------------
152
- (29) → In the bioshell, if "stop?" is issued, then the colouring isn't
167
+ (28) → In the bioshell, if "stop?" is issued, then the colouring isn't
153
168
  correct. It currently does not show any result. This has to
154
169
  be fixed.
155
170
  --------------------------------------------------------------------------------
156
- (30) → https://www.rubydoc.info/gems/biomart
171
+ (29) → https://www.rubydoc.info/gems/biomart
157
172
  ^^^ integrate biomart
158
173
  p biomart.list_datasets
159
174
  p biomart.datasets?
160
175
  --------------------------------------------------------------------------------
161
- (31) → Add Trypsin und Trypsinogen sequences, both as FASTA
176
+ (30) → Add Trypsin und Trypsinogen sequences, both as FASTA
162
177
  but also as shortcut via the commandline such as:
163
178
  show_orf :trypsine
164
179
  show_orf :trypsin
165
180
  Or something like this; and document it as well.
166
181
  --------------------------------------------------------------------------------
167
- (32) → 1..60
182
+ (31) → 1..60
168
183
  setdna 57
169
184
  append stop
170
185
  1..60
@@ -174,12 +189,12 @@
174
189
  ^^^ hier beim colourize, wenn das letzte codon ein STOP codon ist
175
190
  dann colourizen wir das auch.
176
191
  --------------------------------------------------------------------------------
177
- (33) → MG1655
192
+ (32) → MG1655
178
193
  ^^^ input this to download the sequence. Also show it to the user.
179
194
  --------------------------------------------------------------------------------
180
- (34) → extend virus-information into the bioroebe project.
195
+ (33) → extend virus-information into the bioroebe project.
181
196
  --------------------------------------------------------------------------------
182
- (35) → Add a way to analyse the chemical structure of all
197
+ (34) → Add a way to analyse the chemical structure of all
183
198
  aminoacids. We wish to show the chemical formula.
184
199
  E. g. if we input:
185
200
  "phenylalanin"
@@ -189,22 +204,22 @@
189
204
  I don't understand why it removes H and 0 so perhaps
190
205
  dont remove that part. But still show the -R.
191
206
  --------------------------------------------------------------------------------
192
- (36) → FIX THE COLOURIZATION BUG; THIS ONE TRIGGERED THE WHOLE
207
+ (35) → FIX THE COLOURIZATION BUG; THIS ONE TRIGGERED THE WHOLE
193
208
  REWRITE AFTER ALL!
194
209
  --------------------------------------------------------------------------------
195
- (37) → FIX TAXONOMY related-problems AS WELL
210
+ (36) → FIX TAXONOMY related-problems AS WELL
196
211
  ^^^^^^ AND DOCUMENT THIS related-problems.
197
212
  --------------------------------------------------------------------------------
198
- (38) → Do note that z will then be a String, not a sequence object anymore.
213
+ (37) → Do note that z will then be a String, not a sequence object anymore.
199
214
  (This may be subject to change in the future, but for now, aka
200
215
  **February 2020**, it is that way.)
201
216
  ^^^^
202
217
  --------------------------------------------------------------------------------
203
- (39) → ^^^ colours are appended. That should not be the case!
218
+ (38) → ^^^ colours are appended. That should not be the case!
204
219
  ADD SOMETHING NEW ... some todo entries
205
220
  and some python tool
206
221
  --------------------------------------------------------------------------------
207
- (40) → rewrite the whole project anew
222
+ (39) → rewrite the whole project anew
208
223
  - improve the documentation
209
224
  - focus on class Protein first and add
210
225
  all_dna_combinations or somethingl ike
@@ -212,7 +227,7 @@
212
227
  .backtrans
213
228
  .reverse_translate
214
229
  --------------------------------------------------------------------------------
215
- (41) →
230
+ (40) →
216
231
  Reduced alphabets for proteins | [not implemented yet]
217
232
  ^^^ check this as well
218
233
  require 'bioroebe/base/commandline_application/aminoacids.rb'
@@ -235,9 +250,9 @@
235
250
  efetch "https://www.ncbi.nlm.nih.gov/gene/744779"
236
251
  ^^^ test this. again
237
252
  --------------------------------------------------------------------------------
238
- (42) → fix tk-levensthein
253
+ (41) → fix tk-levensthein
239
254
  --------------------------------------------------------------------------------
240
- (43) → rewrite the whole project anew
255
+ (42) → rewrite the whole project anew
241
256
  - improve the documentation
242
257
  - rework the WHOLE tutorial as well
243
258
  - focus on class Protein first and add
@@ -246,12 +261,12 @@
246
261
  .backtrans
247
262
  .reverse_translate
248
263
  --------------------------------------------------------------------------------
249
- (44) → analyze /Depot/Temp/Bioroebe/1CEZ.pdb
264
+ (43) → analyze /Depot/Temp/Bioroebe/1CEZ.pdb
250
265
  ^^^
251
266
  support this. Already works half-way, we started writing a pdb parser.
252
267
  this should work in general, for .fasta files as well.
253
268
  --------------------------------------------------------------------------------
254
- (45) → SINATRA STUFF:
269
+ (44) → SINATRA STUFF:
255
270
  FIX AND EXTEND SINATRA IN BIOROEBE.
256
271
  extend it too.
257
272
  http://localhost:4567/random_aminoacids
@@ -261,7 +276,7 @@
261
276
  where the nucleotide sequence has numbers
262
277
  ^^^
263
278
  --------------------------------------------------------------------------------
264
- (46) → pick any virus and begin to amass tons of data; and then when done
279
+ (45) → pick any virus and begin to amass tons of data; and then when done
265
280
  also connect this into a GUI for use therein.
266
281
  See:
267
282
  https://raw.githubusercontent.com/labsquare/fastQt/master/screenshot.gif
@@ -272,15 +287,15 @@
272
287
  research about circovirus too
273
288
  https://www.ncbi.nlm.nih.gov/nuccore/NC_038391.1
274
289
  --------------------------------------------------------------------------------
275
- (47) → Fix:
290
+ (46) → Fix:
276
291
  require 'bioroebe/toplevel_methods/open_reading_frames.rb'
277
292
  Something is wrong; it returns regions that contain
278
293
  a stop codon, which can not be true.
279
294
  --------------------------------------------------------------------------------
280
- (48) → Fix: extend glycovirology parts
295
+ (47) → Fix: extend glycovirology parts
281
296
  seek stuff in viral genomes
282
297
  --------------------------------------------------------------------------------
283
- (49) →
298
+ (48) →
284
299
  seq = Bio::Sequence::NA.new("atgcatgcaaaaaaa")
285
300
  puts seq
286
301
  puts seq.complement
@@ -302,7 +317,7 @@
302
317
  puts seq
303
318
  puts seq.complement
304
319
  --------------------------------------------------------------------------------
305
- (50) → In BioRoebe:
320
+ (49) → In BioRoebe:
306
321
  Add a table showing how compatible bioroebe is compared to the other
307
322
  bio-projects, staring with biophp.
308
323
  Also show the status how much is complete in each,
@@ -310,7 +325,7 @@
310
325
  And add a table which functionality is implemented
311
326
  in Java already.
312
327
  --------------------------------------------------------------------------------
313
- (51) →
328
+ (50) →
314
329
  ********************************************************************************
315
330
  Was passiert wenn wir das Lambda-Genom mit EcoRI behandeln?
316
331
  ********************************************************************************
@@ -329,11 +344,11 @@
329
344
  ^^^ this now works kind of ... but it must be better
330
345
  documented and we must test this with more data.
331
346
  --------------------------------------------------------------------------------
332
- (52) → https://international.neb.com/products/r0196-ncii#Product%20Information
347
+ (51) → https://international.neb.com/products/r0196-ncii#Product%20Information
333
348
  ^^^ autogenerate such an image, aka restriction cutting enzyme
334
349
  to indicate the target sequence.
335
350
  --------------------------------------------------------------------------------
336
- (53) → how to do codon optimiation in e.coli? bioroebe must support this!
351
+ (52) → how to do codon optimiation in e.coli? bioroebe must support this!
337
352
  we must first get a display which codon is very commonly used in
338
353
  E. coli, from some remote site ... japanese site I think.
339
354
  then, we analyse all possibilities.
@@ -341,19 +356,19 @@
341
356
  them on the commandline
342
357
  class: OptimizeCodons.new(of_this_sequence)
343
358
  --------------------------------------------------------------------------------
344
- (54) → Molekulare Grösse von "Ubiquitin"? "8.5 kd".
359
+ (53) → Molekulare Grösse von "Ubiquitin"? "8.5 kd".
345
360
  ^^^ das sollte automatisch ausgerechnet werden
346
361
  --------------------------------------------------------------------------------
347
- (55) → taxonomy !!!!!!!!!!!!!!!!!!
362
+ (54) → taxonomy !!!!!!!!!!!!!!!!!!
348
363
  --------------------------------------------------------------------------------
349
- (56) → Given a list of gene names that I would like to get chromosome/position
364
+ (55) → Given a list of gene names that I would like to get chromosome/position
350
365
  information for (in mm10). Is there some service online where I can
351
366
  paste this list? ^^^ enable this
352
367
  --------------------------------------------------------------------------------
353
- (57) → Make bioroebe very useful from the www, no matter if via sinatra
368
+ (56) → Make bioroebe very useful from the www, no matter if via sinatra
354
369
  or rails. It should be a tool-set project on the www as well.
355
370
  --------------------------------------------------------------------------------
356
- (58) → Suppose you have a GenBank file which you want to turn into a
371
+ (57) → Suppose you have a GenBank file which you want to turn into a
357
372
  Fasta file. For example, lets consider the file cor6_6.gb
358
373
  which is included in the Biopython unit tests under the
359
374
  GenBank directory.
@@ -364,26 +379,26 @@
364
379
  the GUI works somewhat but needs to be polished up.
365
380
  THEN THIS CAN BE REMOVED!!!!!!!
366
381
  --------------------------------------------------------------------------------
367
- (59) → Wir brauchen eine table wo wir die starken promotoren verschiedener
382
+ (58) → Wir brauchen eine table wo wir die starken promotoren verschiedener
368
383
  Organismen zusammenstellen und vergleichen können.
369
384
  strong_promoters.yml
370
385
  --------------------------------------------------------------------------------
371
- (60) → add:
386
+ (59) → add:
372
387
  start position of exons
373
388
  and show the sequence based on that file
374
389
  Normally there's a "gene" entry for each gene, so:
375
390
  awk 'BEGIN{FS="\t"; OFS="\t"}{if($3 == "gene") print $1, $4, $5}' foo.gtf
376
391
  --------------------------------------------------------------------------------
377
- (61) → also add 30-33 to aminoacids hmmm difficult.
392
+ (60) → also add 30-33 to aminoacids hmmm difficult.
378
393
  --------------------------------------------------------------------------------
379
- (62) → http://bioinformatics.oxfordjournals.org/content/18/8/1135
394
+ (61) → http://bioinformatics.oxfordjournals.org/content/18/8/1135
380
395
  "TFBS: Computational framework for transcription factor
381
396
  binding site analysis"
382
397
  study the above and see if it can be included
383
398
  into bioroebe
384
399
  http://tfbs.genereg.net/
385
400
  --------------------------------------------------------------------------------
386
- (63) → They include trypsin, chymotrypsin, thrombin, plasmin, papain and factor Xa.
401
+ (62) → They include trypsin, chymotrypsin, thrombin, plasmin, papain and factor Xa.
387
402
  ^^^ provide means to identify where they cut,
388
403
  and show this then by simualting a digest.
389
404
  return an array with the starting aminoacids.
@@ -391,7 +406,7 @@
391
406
  this is done via digestion/digestions
392
407
  but it's not quite perfect yet.
393
408
  --------------------------------------------------------------------------------
394
- (64) → a) add a commandline way to generate a random protein
409
+ (63) → a) add a commandline way to generate a random protein
395
410
  with a specified length and then display it on the
396
411
  commandline [DONE] !!!
397
412
  bioroebe --random-aminoacids=33
@@ -411,26 +426,26 @@
411
426
  Enable this BOTH from the commandline AND from the
412
427
  interactive variant and from sinatra! Hmmmm.
413
428
  --------------------------------------------------------------------------------
414
- (65) → add an option to design a
429
+ (64) → add an option to design a
415
430
  degenerate primer
416
431
  --------------------------------------------------------------------------------
417
- (66) → Add upcase to sequences and ensure that it works; also document it
432
+ (65) → Add upcase to sequences and ensure that it works; also document it
418
433
  internally and in the .pdf tutorial
419
434
  what does that mean? upcase as method? hmmm.
420
435
  --------------------------------------------------------------------------------
421
- (67) → http://www.biomart.org/other/user-docs.pdf
436
+ (66) → http://www.biomart.org/other/user-docs.pdf
422
437
  ^^^ work through this
423
438
  ^^^ integrate the old .cgi part and improve as you go
424
439
  --------------------------------------------------------------------------------
425
- (68) → Access geninfo numbers easily.
440
+ (67) → Access geninfo numbers easily.
426
441
  Die suchen und runterladen.
427
442
  --------------------------------------------------------------------------------
428
- (69) → Add all of bioruby into bioroebe:
443
+ (68) → Add all of bioruby into bioroebe:
429
444
  continous project
430
445
  https://github.com/biopython/biopython
431
446
  https://github.com/bioruby/bioruby/tree/master/lib/bio
432
447
  --------------------------------------------------------------------------------
433
- (70) → https://github.com/bioruby/bioruby/issues/134
448
+ (69) → https://github.com/bioruby/bioruby/issues/134
434
449
  ^^^ check this, for restriction enzymes
435
450
  http://rebase.neb.com/rebase/enz/MboII.html
436
451
  Bio::RestrictionEnzyme.cut(seq, 'MboII').primary rescue [seq]
@@ -439,9 +454,9 @@
439
454
  > Bio::RestrictionEnzyme.cut(seq, 'MboII').primary rescue [seq]
440
455
  => ["atcatcaatcctaatcttct"]
441
456
  --------------------------------------------------------------------------------
442
- (71) → Document how an ORF is defined for the bioroebe project.
457
+ (70) → Document how an ORF is defined for the bioroebe project.
443
458
  --------------------------------------------------------------------------------
444
- (72) → Continue with biojava in bioroebe.
459
+ (71) → Continue with biojava in bioroebe.
445
460
  → We need to make some table that tells us what is implemented
446
461
  in java.
447
462
  → Make it possible to randomly generate aminoacids, and then,
@@ -451,7 +466,7 @@
451
466
  We can generate degenerate primers now:
452
467
  dprimer M-T-T-Y-Y-T-A-A-A-STOP
453
468
  --------------------------------------------------------------------------------
454
- (73) → The codon tables:
469
+ (72) → The codon tables:
455
470
  → In January we added a codon-table GUI to ruby-gtk3.
456
471
  also enable an inverse table.
457
472
  Ala/A GCT, GCC, GCA, GCG GCN Leu/L TTA, TTG, CTT, CTC, CTA, CTG YTR, CTN
@@ -474,26 +489,26 @@
474
489
  that we can now display all the different codon tables.
475
490
  This now sorta works semi-ok.
476
491
  --------------------------------------------------------------------------------
477
- (74) → In the bioroebe-shell, enable input such as:
492
+ (73) → In the bioroebe-shell, enable input such as:
478
493
  NC_000011.10
479
494
  This shall quickly download this sequence into the
480
495
  local file, and also rename it properly.
481
496
  --------------------------------------------------------------------------------
482
- (75) → clone all of bioruby
497
+ (74) → clone all of bioruby
483
498
  --------------------------------------------------------------------------------
484
- (76) → bioinf bücher udrhclesen und zeug inkludiere !!!
499
+ (75) → bioinf bücher udrhclesen und zeug inkludiere !!!
485
500
  ^^^^^ mehr bilderchen hinzufügen ... auchv on den GUIs eventuell.
486
501
  Und auch biopython durcharbeiten und alles wichtige nach
487
502
  bioroebe übertragen.
488
503
  --------------------------------------------------------------------------------
489
- (77) → Add: DetectMotif
504
+ (76) → Add: DetectMotif
490
505
  This class shall be used for detecting subsequences.
491
506
  --------------------------------------------------------------------------------
492
- (78) → Neue funktionälit rein
507
+ (77) → Neue funktionälit rein
493
508
  --------------------------------------------------------------------------------
494
- (79) → mehr doku!!!
509
+ (78) → mehr doku!!!
495
510
  --------------------------------------------------------------------------------
496
- (80) → Rewrite bioroebe completely - add some tests, too or so, to
511
+ (79) → Rewrite bioroebe completely - add some tests, too or so, to
497
512
  test this. ^^^
498
513
  That way we learn how to write tests.
499
514
  AND ... we will actually start with the taxonomy project
@@ -533,7 +548,7 @@
533
548
  also add a footer to show which entries are available or so
534
549
  → in bioroebe, mach das die postgresql datenbank wieder funktioniert ...
535
550
  --------------------------------------------------------------------------------
536
- (81) → ^^^ improve this whole project a lot
551
+ (80) → ^^^ improve this whole project a lot
537
552
  before uploading then send email
538
553
  → add:
539
554
  set_dna :insulin
@@ -546,28 +561,28 @@
546
561
  → becomes: http://www.ncbi.nlm.nih.gov/gene/3630
547
562
  wtf ... better to learn how NCBI uworks
548
563
  --------------------------------------------------------------------------------
549
- (82) → Add a seuqence table into bioroebe for GFP, YFP etc
564
+ (81) → Add a seuqence table into bioroebe for GFP, YFP etc
550
565
  and mae this show in both the interactio bioshell but
551
566
  also the main README.md
552
567
  --------------------------------------------------------------------------------
553
- (83) → http://www.biophp.org/stats/describe_data/demo.php?show=formula
568
+ (82) → http://www.biophp.org/stats/describe_data/demo.php?show=formula
554
569
  ^^^ should also add documentation like this, also via www interface
555
570
  --------------------------------------------------------------------------------
556
- (84) → Add a "cutter-range example" in restriction enzymes +
571
+ (83) → Add a "cutter-range example" in restriction enzymes +
557
572
  table + examples + tutorial
558
573
  one example each in this overview.
559
574
  Also, add in the documentation where this
560
575
  can be found.
561
576
  --------------------------------------------------------------------------------
562
- (85) → Add some codon-usage analyzer. What shall it show? It
577
+ (84) → Add some codon-usage analyzer. What shall it show? It
563
578
  should show how many codons are used, frequencies etc...
564
579
  by an organism, and compare that to other data.
565
580
  --------------------------------------------------------------------------------
566
- (86) → Implement a GPCR interface.
581
+ (85) → Implement a GPCR interface.
567
582
  This is for "G-protein coupled receptors."
568
583
  Denote which variants exist and so forth. Document it as well.
569
584
  --------------------------------------------------------------------------------
570
- (87) → alu?
585
+ (86) → alu?
571
586
  Will read from the file `/Programs/Ruby/2.3.0/lib/ruby/site_ruby/2.3.0/bioroebe/yaml/alu_elements.yml`.
572
587
  Bioroebe::ParseFasta: This sequence is assumed to be a protein.
573
588
  This sequence has 1317 aminoacids.
@@ -583,7 +598,7 @@
583
598
  And perhaps add a small protein as an example how to
584
599
  work with .pdb files instead.
585
600
  --------------------------------------------------------------------------------
586
- (88) → Extend bioroebe to allow download
601
+ (87) → Extend bioroebe to allow download
587
602
  PDB files
588
603
  id 3030
589
604
  and then display nice thingies to the user.
@@ -592,35 +607,35 @@
592
607
  in 3EML 2VTP 2VEZ
593
608
  do
594
609
  --------------------------------------------------------------------------------
595
- (89) → Fully integrate electron microscopy then remove the old entry.
610
+ (88) → Fully integrate electron microscopy then remove the old entry.
596
611
  Test it though.
597
612
  Hmm... but ... we will first polish the main bioroebe
598
613
  gem AND the taxonomy gem and THEN AFTERWARDS
599
614
  integate elctron microsopcy.
600
615
  --------------------------------------------------------------------------------
601
- (90) → ORF Finder:
616
+ (89) → ORF Finder:
602
617
  We must add an ORF finder for the bioroebe project,
603
618
  similar to the NCBI ORF Finder.
604
619
  This works partially... start_stop works but we do not
605
620
  yet find all subsequences.
606
621
  --------------------------------------------------------------------------------
607
- (91) → must change determine whether we have protein or nucleotide or
622
+ (90) → must change determine whether we have protein or nucleotide or
608
623
  so via a topelvel method!
609
624
  --------------------------------------------------------------------------------
610
- (92) → there is a talens module.
625
+ (91) → there is a talens module.
611
626
  we have to improve on it for a while
612
627
  better docu
613
628
  more testing
614
629
  then we can get rid of this entry here
615
630
  --------------------------------------------------------------------------------
616
- (93) → 33.44
631
+ (92) → 33.44
617
632
  Next showing the nucleotides 33 to 44 (including 33 and 44).
618
633
  The length of the fragment will be 12 nucleotides.
619
634
  5' - 2;70;130;180 - 3'
620
635
  ^^^ there is some problem; we somehow embed the colour codes,
621
636
  which should not happen.
622
637
  --------------------------------------------------------------------------------
623
- (94) → set_aa DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STASSWSYIV ETSNSDNGTC YPGDFINYEE LREQLSSVSS FERFEIFPKT SSWPNHDNKG VTAACPHAGA KSFYKNLIWL VKKGNSYPKL NQSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADAYVFV GTSRYSKKFK PEIATRPKVR DQEGRMNYYW TLVEPGDKIT FEATGNLVVP RYAFMERNAG SGIIISDTPV HDCNTTCQTP EGAINTSLPF QNIHPITIGK CPKYVKSTKL RLATGLRNVP SIQSRGLFGA IAGFIEGGWT GMVDGWYGYH HQNEQGSGYA ADLKSTQNAI DKITNKVNSV IKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRNQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREKIDGV KLESTRIYHH HHHH
638
+ (93) → set_aa DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STASSWSYIV ETSNSDNGTC YPGDFINYEE LREQLSSVSS FERFEIFPKT SSWPNHDNKG VTAACPHAGA KSFYKNLIWL VKKGNSYPKL NQSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADAYVFV GTSRYSKKFK PEIATRPKVR DQEGRMNYYW TLVEPGDKIT FEATGNLVVP RYAFMERNAG SGIIISDTPV HDCNTTCQTP EGAINTSLPF QNIHPITIGK CPKYVKSTKL RLATGLRNVP SIQSRGLFGA IAGFIEGGWT GMVDGWYGYH HQNEQGSGYA ADLKSTQNAI DKITNKVNSV IKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRNQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREKIDGV KLESTRIYHH HHHH
624
639
  ^^^ enable copy/pasting,
625
640
  then reverse_sequence
626
641
  dna_sequence?
@@ -631,7 +646,7 @@
631
646
  This sequence has 50 aminoacids.
632
647
  ^^^ das stimmt net.
633
648
  --------------------------------------------------------------------------------
634
- (95) → add this functionality:
649
+ (94) → add this functionality:
635
650
  meting temper
636
651
  melting temper
637
652
  melting_temperature?
@@ -659,44 +674,44 @@
659
674
  using ruby. The latter may be useful and rather easy for
660
675
  scripted use.
661
676
  --------------------------------------------------------------------------------
662
- (96) → show insulin
677
+ (95) → show insulin
663
678
  ^^^ to show the insulin structure
664
679
  how to find it? no idea...
665
680
  but we should have these structures already made available somewhere.
666
681
  --------------------------------------------------------------------------------
667
- (97) → Todo: find family of enzymes, based on sequence structure
682
+ (96) → Todo: find family of enzymes, based on sequence structure
668
683
  alone.
669
684
  --------------------------------------------------------------------------------
670
- (98) → WORK THROUGH the PROTOCOL AT BOKU. THEN WORK THROUGH THE VARIOUST
685
+ (97) → WORK THROUGH the PROTOCOL AT BOKU. THEN WORK THROUGH THE VARIOUST
671
686
  TIDBIDS AT UNI WIEN STARTING WITH HEIKO.
672
687
  ^^^ da sind wir nun.
673
688
  wir sind an beginn von 1b ... hmmmm, also zerst mal das an der
674
689
  BOKU durchgehen. Dann das löschen.
675
690
  --------------------------------------------------------------------------------
676
- (99) → Begin tk-bindings for bioroebe, following the gtk stuff.
691
+ (98) → Begin tk-bindings for bioroebe, following the gtk stuff.
677
692
  --------------------------------------------------------------------------------
678
- (100) → frame_value = position_of_the_stop_codon - position_of_the_start_codon
693
+ (99) → frame_value = position_of_the_stop_codon - position_of_the_start_codon
679
694
  ^^^ continue on this ...
680
695
  --------------------------------------------------------------------------------
681
- (101) → improve both the gtk-apps parts, and the sinatra web-interface,
696
+ (100) → improve both the gtk-apps parts, and the sinatra web-interface,
682
697
  and other GUI-like elements. The idea is to make this software
683
698
  more useful for people around the world, which should help
684
699
  increase its adoption rate.
685
700
  --------------------------------------------------------------------------------
686
- (102) → Look to integrate this:
701
+ (101) → Look to integrate this:
687
702
  http://www.ncbi.nlm.nih.gov/nuccore/NM_007315.3?report=fasta&log$=seqview&format=text
688
703
  ^^^
689
704
  --------------------------------------------------------------------------------
690
- (103) → We need to make available the ... thingy magick
705
+ (102) → We need to make available the ... thingy magick
691
706
  emboss functionality. that may seem useful
692
707
  but also feel free to extend these parts for
693
708
  bioroebe as necessary.
694
709
  --------------------------------------------------------------------------------
695
- (104) → integrate electron_microscopy fully
710
+ (103) → integrate electron_microscopy fully
696
711
  This will take more time, so first we finish with the
697
712
  taxonomy module instead.
698
713
  --------------------------------------------------------------------------------
699
- (105) → Improve support for BLAST up until
714
+ (104) → Improve support for BLAST up until
700
715
  middle of 2015 so that I am better prepared
701
716
  for work-related stuff. In order for this
702
717
  to succed, we first have to understand
@@ -704,14 +719,14 @@
704
719
  So, work on BLAST tutorial at bioinf page:
705
720
  bl bioinf; rf bioinf
706
721
  --------------------------------------------------------------------------------
707
- (106) → integrate a "codon usage database", whatever this means.
722
+ (105) → integrate a "codon usage database", whatever this means.
708
723
  It is a cool database anyway. Then document this.
709
724
  First, create a codon-usage analyze on a per-FASTA
710
725
  site basis. Meaning we download a fasta sequence
711
726
  and calculate the codon usage from there.
712
727
  ^^^ and add some GUI to this. hmmm
713
728
  --------------------------------------------------------------------------------
714
- (107) → Input sequence:
729
+ (106) → Input sequence:
715
730
  MFLMVSPTAYHQNKDECFLP
716
731
  TAYHQNKDECMVSPTAYHQN
717
732
  KDECFLPTAYHQMVSPTAYH
@@ -724,42 +739,42 @@
724
739
  ^^^ we should also show this on the commandline AND the
725
740
  www ... hmmm.
726
741
  --------------------------------------------------------------------------------
727
- (108) → enable a graphical layer so that we can find out which
742
+ (107) → enable a graphical layer so that we can find out which
728
743
  transcription factor activates which gene(s). This
729
744
  should show e. g. a transcription factor highlighting
730
745
  a target genetic area.
731
746
  --------------------------------------------------------------------------------
732
- (109) → We should add more screenshots, make them available on imgur
747
+ (108) → We should add more screenshots, make them available on imgur
733
748
  as well, after storing them locally. Start with the more
734
749
  important functionality.
735
750
  --------------------------------------------------------------------------------
736
- (110) → clone serial cloner or whatever the name was, that GUI,
751
+ (109) → clone serial cloner or whatever the name was, that GUI,
737
752
  so that we can offer the same functionality.
738
753
  --------------------------------------------------------------------------------
739
- (111) →
754
+ (110) →
740
755
  # * searching for PubMed IDs given a query string:
741
756
  # * Bio::PubMed#esearch (recommended)
742
757
  # * Bio::PubMed#search (only retrieves top 20 hits; will be deprecated)
743
758
  ^^^ implement this
744
759
  --------------------------------------------------------------------------------
745
- (112) → Aufgabe 16 in bioroebe lösen könnnen
760
+ (111) → Aufgabe 16 in bioroebe lösen könnnen
746
761
  --------------------------------------------------------------------------------
747
- (113) → re1 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme1)
762
+ (112) → re1 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme1)
748
763
  ^^^ add this? hmmmm
749
764
  ^^^ from here.
750
765
  --------------------------------------------------------------------------------
751
- (114) → Colourize exon/intron boundaries.
766
+ (113) → Colourize exon/intron boundaries.
752
767
  --------------------------------------------------------------------------------
753
- (115) → In bioroebe: enhance phylogeny stuff and perhaps automatically
768
+ (114) → In bioroebe: enhance phylogeny stuff and perhaps automatically
754
769
  generate pictures here.
755
770
  --------------------------------------------------------------------------------
756
- (116) → In sinatra: add a backtranseq entry point, perhaps
771
+ (115) → In sinatra: add a backtranseq entry point, perhaps
757
772
  alias it as well.
758
773
  ^^ sync this to ruby-gtk3? hmm
759
774
  bioroebe --protein-to-dna
760
775
  ^^^ this shall start the GTK3 variant
761
776
  --------------------------------------------------------------------------------
762
- (117) → require 'rubygems/text'
777
+ (116) → require 'rubygems/text'
763
778
  include Gem::Text
764
779
  levenshtein_distance 'shevy', 'chevy' # => 1
765
780
  ^^^ add some class that outpus, on the commandline
@@ -768,13 +783,13 @@
768
783
  https://github.com/rubygems/rubygems/blob/master/lib/rubygems/text.rb
769
784
  ^^^ actually move that part into bioroebe itself...
770
785
  --------------------------------------------------------------------------------
771
- (118) → add _source to all APIs in sinatra there. Ensure that this works
786
+ (117) → add _source to all APIs in sinatra there. Ensure that this works
772
787
  too. The user should be able to view the source code.
773
788
  ^^^ it has been added for 2 methods so far in sinatra; we need
774
789
  to add it for the remaining ones too. Then we can remove
775
790
  this entry point.
776
791
  --------------------------------------------------------------------------------
777
- (119) → Check out expasy
792
+ (118) → Check out expasy
778
793
  peptidcutter
779
794
  also offer this functionality, through commandline, GUI
780
795
  and sinatra.
@@ -782,18 +797,18 @@
782
797
  We now have added trypsin but we should add more here; and
783
798
  still have to add support for sinatra here.
784
799
  --------------------------------------------------------------------------------
785
- (120) → melting temperature subsection
800
+ (119) → melting temperature subsection
786
801
  hmmm .... molecular weight calculation works now ... but
787
802
  ... is it correct for a ssDNA string? hmm...
788
803
  --------------------------------------------------------------------------------
789
- (121) → Degenerate Primers
804
+ (120) → Degenerate Primers
790
805
  You can try to determine the degenerate primers via the Shell
791
806
  component. Issue the following instructions:
792
807
  degenerate_primer
793
808
  ^^^ epxnad that subsection
794
809
  more explanations and examples
795
810
  --------------------------------------------------------------------------------
796
- (122) → Copy the functionality of plotorf:
811
+ (121) → Copy the functionality of plotorf:
797
812
  See:
798
813
  http://www.bioinformatics.nl/cgi-bin/emboss/plotorf
799
814
  Also extend emboss info on the main homepage.
@@ -803,44 +818,44 @@
803
818
  ^^^
804
819
  Bioroebe.return_all_ORFS
805
820
  --------------------------------------------------------------------------------
806
- (123) → Start nucleotide position is at: 142
821
+ (122) → Start nucleotide position is at: 142
807
822
  See the following example:
808
823
  BIO SHELL> highlight AAA
809
824
  5' - GTAACTGTTAAACTGTCAGGCAGGCGCTCAGGTGTACGTTTGATGCTCAGTAGTATTCCATTCTCGCGAGGGTCACGATACCCAAGATCTCCATGGCTTTCTGTTAGACGCAGCCGTGGACGACTAGAGCGTTTTTTTTTGGAAAGTATATGACCAGCACTCTACATCCTAACTAGAAGGTCTTCTAGGCGTACCAATATTAACGAATAGTGAGTGGTTACCCGTACCCGTCATGACGTCTATCATTAATT - 3'
810
825
  BIO SHELL>
811
826
  ^^^ this does not work; nothing is highlighted.
812
827
  --------------------------------------------------------------------------------
813
- (124) → Add a myristoylierung-signal
828
+ (123) → Add a myristoylierung-signal
814
829
  Met-Gly-Xaa-Xaa-YXaa-Ser/Thr-Lys-Lys
815
830
  1^^ but check first.
816
831
  --------------------------------------------------------------------------------
817
- (125) → integrate the bioroebe_tutorial.cgi into the .md file completely.
832
+ (124) → integrate the bioroebe_tutorial.cgi into the .md file completely.
818
833
  --------------------------------------------------------------------------------
819
- (126) → Integrate everything from the biopython tutorial, if it makes
834
+ (125) → Integrate everything from the biopython tutorial, if it makes
820
835
  sense.
821
836
  --------------------------------------------------------------------------------
822
- (127) → Improve the codon-optimizer in Bioroebe, including the
837
+ (126) → Improve the codon-optimizer in Bioroebe, including the
823
838
  documentation. We need to make this really useful.
824
839
  --------------------------------------------------------------------------------
825
- (128) →
840
+ (127) →
826
841
  5'- TACACGGCACAT -3'
827
842
  3'- ATGTGCCGTGTA -5'
828
843
  Imperfect DNA mirror repeats (IMRs) are less than 100% symmetrical.
829
844
  ^^^ integrate mirror repeats creation
830
845
  and searching for them. Hmmm.
831
846
  --------------------------------------------------------------------------------
832
- (129) → continue porting bioroebe/taxonomy
847
+ (128) → continue porting bioroebe/taxonomy
833
848
  ^^^^^^^^^^
834
849
  It has been 5 years ...
835
850
  ^^^ taxonomy/colours/colours wird integriert
836
851
  ^^^ das ist der nächste schritt, so das
837
852
  wir das nit mehr benötigen.
838
853
  --------------------------------------------------------------------------------
839
- (130) → find out which bacteria all contain the needle complex; find out
854
+ (129) → find out which bacteria all contain the needle complex; find out
840
855
  the sequence for the needle complex as well and study it;
841
856
  find the positions of the genes responsible.
842
857
  --------------------------------------------------------------------------------
843
- (131) → Add trypsin_digest, also in the shell, but possibly
858
+ (130) → Add trypsin_digest, also in the shell, but possibly
844
859
  on toplevel as well (if the input is a protein sequence.
845
860
  Also, more generally in the shell, add this:
846
861
  digest trypsin
@@ -850,22 +865,22 @@
850
865
  follows !!!
851
866
  ^^^ document this too into .md
852
867
  --------------------------------------------------------------------------------
853
- (132) → add codon usage in bioroebe
868
+ (131) → add codon usage in bioroebe
854
869
  --------------------------------------------------------------------------------
855
- (133) → Clone the following functionality.
870
+ (132) → Clone the following functionality.
856
871
  http://www.bioinformatics.nl/cgi-bin/emboss/help/sirna
857
872
  --------------------------------------------------------------------------------
858
- (134) → Improve the "find and scan" subsection. We must be able to find
873
+ (133) → Improve the "find and scan" subsection. We must be able to find
859
874
  subsequences; check for "matches" as well, including the bioshell.
860
875
  --------------------------------------------------------------------------------
861
- (135) → Clone the CLUSTAL format aligment.
876
+ (134) → Clone the CLUSTAL format aligment.
862
877
  --------------------------------------------------------------------------------
863
- (136) → We need to be able to load up a whole geneome into bioroebe,
878
+ (135) → We need to be able to load up a whole geneome into bioroebe,
864
879
  and then be able to manipulate it.
865
880
  ^^^ perhaps test this with some example
866
881
  data or so...
867
882
  --------------------------------------------------------------------------------
868
- (137) → Restriction enzymes:
883
+ (136) → Restriction enzymes:
869
884
  Add a subsection about restritction enzymes including
870
885
  examples, and also explain how to use this in bioroebe.
871
886
  Minute by minute...
@@ -875,7 +890,7 @@
875
890
  general, so that we can reproduce and verify the
876
891
  information there.
877
892
  --------------------------------------------------------------------------------
878
- (138) → clone pepinfo
893
+ (137) → clone pepinfo
879
894
  The program "pepinfo" plots various amino acid properties in
880
895
  parallel for an input protein sequence.
881
896
  The types of plot available are:
@@ -887,7 +902,7 @@
887
902
  Charged, Positive, Negative.
888
903
  The data are also written out to an output file.
889
904
  --------------------------------------------------------------------------------
890
- (139) → gff?
905
+ (138) → gff?
891
906
  There are 6 .gff3 files in the current directory.
892
907
  We will simply pass the first entry there into class Bioroebe::Parser::GFF.
893
908
  The accession id is `NZ_CP011602.1`.
@@ -896,39 +911,39 @@
896
911
  Bioroebe::Parser::GFF: in this file.
897
912
  ^^^ we need an analyze-mode as well.
898
913
  --------------------------------------------------------------------------------
899
- (140) → ^^^^ add the ability to
914
+ (139) → ^^^^ add the ability to
900
915
  show a ruler AND highlighting as well
901
916
  ^^^ then document it.
902
917
  --------------------------------------------------------------------------------
903
- (141) → https://github.com/bioperl/bioperl-live
918
+ (140) → https://github.com/bioperl/bioperl-live
904
919
  Look what we can take from ^^^.
905
920
  https://github.com/bioperl/bioperl-live/tree/master/examples
906
921
  --------------------------------------------------------------------------------
907
- (142) → continue biojava, and bioroebe a bit
922
+ (141) → continue biojava, and bioroebe a bit
908
923
  Ideally we should have biojava o a working point.
909
924
  --------------------------------------------------------------------------------
910
- (143) → clone the functionality found at https://web.expasy.org/protparam/
925
+ (142) → clone the functionality found at https://web.expasy.org/protparam/
911
926
  https://web.expasy.org/cgi-bin/protparam/protparam
912
927
  ^^^ this is halfway done...
913
928
  ^^^^ also add pI calculation:
914
929
  Theoretical pI: 5.78
915
930
  --------------------------------------------------------------------------------
916
- (144) → NP_417539.1
931
+ (143) → NP_417539.1
917
932
  https://www.ncbi.nlm.nih.gov/protein/NP_417539.1
918
933
  https://www.ncbi.nlm.nih.gov/protein/NP_417539.1?report=fasta
919
934
  ^^^ if the input is exactly like the above, on the first line,
920
935
  download the sequence.
921
936
  --------------------------------------------------------------------------------
922
- (145) → http://www.biostars.org/
937
+ (144) → http://www.biostars.org/
923
938
  ^^^ regularly work through this
924
939
  and try to help
925
940
  and extend bioruby at the same time.
926
941
  --------------------------------------------------------------------------------
927
- (146) → The taxonomy-submodule should work one day, and be properly
942
+ (145) → The taxonomy-submodule should work one day, and be properly
928
943
  documented as well. Perhaps integrate the parts of Taxonomy
929
944
  that can be included into the toplevel domain.
930
945
  --------------------------------------------------------------------------------
931
- (147) → Enable:
946
+ (146) → Enable:
932
947
  Bioroebe.set_genetic_code()
933
948
  Bioroebe.set_genetic_code(to: 'Vertebrate Mitochondrial')
934
949
  ^^^ enable this
@@ -939,58 +954,58 @@
939
954
  Seq('MAIVMGRWKGAR*')
940
955
  ^^^ enable this as well; extent documentation too.
941
956
  --------------------------------------------------------------------------------
942
- (148) → We have found a restriction enzyme called NheI.
957
+ (147) → We have found a restriction enzyme called NheI.
943
958
  The sequence this 6-cutter relates to is: `5' - GCTAGC - 3'`
944
959
  This restriction enzyme will produce a blunt overhang.
945
960
  ^^^ nope das ist falsch
946
961
  --------------------------------------------------------------------------------
947
- (149) → Sau3A?
962
+ (148) → Sau3A?
948
963
  ^^^ enable this restriction site
949
964
  --------------------------------------------------------------------------------
950
- (150) → Add matplotlib support.
965
+ (149) → Add matplotlib support.
951
966
  try_to_use_matplotlib
952
967
  --------------------------------------------------------------------------------
953
- (151) → https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/RESTfulAPIs.html
968
+ (150) → https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/RESTfulAPIs.html
954
969
  --------------------------------------------------------------------------------
955
- (152) → The following input:
970
+ (151) → The following input:
956
971
  downcase; orf?; seq?
957
972
  leads to strange display. Something is wrong here, must be checked.
958
973
  --------------------------------------------------------------------------------
959
- (153) → Continue with rosalind problems.
974
+ (152) → Continue with rosalind problems.
960
975
  These challenges can be found here:
961
976
  http://rosalind.info/problems/sign/
962
977
  Also integrate these rosalind-quizzes into bioroebe
963
978
  when possible.
964
979
  --------------------------------------------------------------------------------
965
- (154) → https://web.expasy.org/cgi-bin/peptide_mass/peptide-mass.pl
980
+ (153) → https://web.expasy.org/cgi-bin/peptide_mass/peptide-mass.pl
966
981
  ^^^ make the above usable in sinaitra as well
967
982
  --------------------------------------------------------------------------------
968
- (155) → Integrate a way to search for commonly known promoters:
983
+ (154) → Integrate a way to search for commonly known promoters:
969
984
  promoters?
970
985
  ^^^ this functionality
971
986
  ^^^ this has to be expanded
972
987
  and ...
973
988
  --------------------------------------------------------------------------------
974
- (156) → Integrate:
989
+ (155) → Integrate:
975
990
  http://biotools.nubic.northwestern.edu/OligoCalc.html
976
991
  --------------------------------------------------------------------------------
977
- (157) → Extend the Java part of BioRoebe systematically..
992
+ (156) → Extend the Java part of BioRoebe systematically..
978
993
  What should come next? Let's make a list.
979
994
  → remove_numbers [DONE]
980
995
  --------------------------------------------------------------------------------
981
- (158) → Study gnuplot; one day we have to draw graphs.
996
+ (157) → Study gnuplot; one day we have to draw graphs.
982
997
  --------------------------------------------------------------------------------
983
- (159) → Add a genome browser, both ascii without GUI and also
998
+ (158) → Add a genome browser, both ascii without GUI and also
984
999
  with. In ruby-gtk.
985
1000
  --------------------------------------------------------------------------------
986
- (160) → Clone the functionality of:
1001
+ (159) → Clone the functionality of:
987
1002
  http://www.biophp.org/minitools/restriction_digest/demo.php
988
1003
  --------------------------------------------------------------------------------
989
- (161) → Add the loxP sequence to readme [DONE] and explain this
1004
+ (160) → Add the loxP sequence to readme [DONE] and explain this
990
1005
  better on the main readme; and perhaps also assign
991
1006
  the sequence via the bioshell.
992
1007
  --------------------------------------------------------------------------------
993
- (162) → 33. Cephalodiscidae Mitochondrial UAA-Tyr Code (transl_table=33)
1008
+ (161) → 33. Cephalodiscidae Mitochondrial UAA-Tyr Code (transl_table=33)
994
1009
  AAs = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG
995
1010
  Starts = ---M-------*-------M---------------M---------------M------------
996
1011
  Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
@@ -999,7 +1014,7 @@
999
1014
  ^^^ add a parser, and document it, that can take this input
1000
1015
  and output the corresponding code, in a valid .yml file.
1001
1016
  --------------------------------------------------------------------------------
1002
- (163) → Add to bioroebe the ability to add cloning vectors
1017
+ (162) → Add to bioroebe the ability to add cloning vectors
1003
1018
  and molecular_weight calcuation
1004
1019
  for this
1005
1020
  and also to show the sequence of a vector
@@ -1015,19 +1030,19 @@
1015
1030
  ^^^ we also need a way to find out what resistance genes
1016
1031
  are carried there.
1017
1032
  --------------------------------------------------------------------------------
1018
- (164) → In the lambda genome sequence there are 10 EcoB and
1033
+ (163) → In the lambda genome sequence there are 10 EcoB and
1019
1034
  5 EcoK sites.
1020
1035
  ^^^ verify this too, as an example as well
1021
1036
  --------------------------------------------------------------------------------
1022
- (165) → show restriction sites, composable and compatible with
1037
+ (164) → show restriction sites, composable and compatible with
1023
1038
  serial clone ... hmm
1024
1039
  --------------------------------------------------------------------------------
1025
- (166) → enable:
1040
+ (165) → enable:
1026
1041
  BIOROEBE_USE_COLOURS:
1027
1042
  can be 0 or 1
1028
1043
  what is this?
1029
1044
  --------------------------------------------------------------------------------
1030
- (167) → Burrows-Wheeler-Transform (BWT)
1045
+ (166) → Burrows-Wheeler-Transform (BWT)
1031
1046
  ^^^ add some method here
1032
1047
  Bioroebe.burrows_wheeler_transform
1033
1048
  ^^^ if no '$' char is in the input, then append it
@@ -1037,13 +1052,13 @@
1037
1052
  also test this against my paper-result
1038
1053
  with input being: "GATAG$".
1039
1054
  --------------------------------------------------------------------------------
1040
- (168) → Enable working with several genes... hmm and store that somewhere.
1055
+ (167) → Enable working with several genes... hmm and store that somewhere.
1041
1056
  Something like a per-project workspace thingy.
1042
1057
  --------------------------------------------------------------------------------
1043
- (169) → Add:
1058
+ (168) → Add:
1044
1059
  http://nar.oxfordjournals.org/content/35/suppl_2/W71.long
1045
1060
  --------------------------------------------------------------------------------
1046
- (170) → Now, you may want to translate the nucleotides up to
1061
+ (169) → Now, you may want to translate the nucleotides up to
1047
1062
  the first in frame stop codon, and then stop (as
1048
1063
  happens in nature):
1049
1064
  coding_dna.translate()
@@ -1054,12 +1069,12 @@
1054
1069
  Then continue from here:
1055
1070
  https://people.duke.edu/~ccc14/pcfb/biopython/BiopythonSequences.html
1056
1071
  --------------------------------------------------------------------------------
1057
- (171) → Add:
1072
+ (170) → Add:
1058
1073
  set_dna :Ubiquitin
1059
1074
  set_dna :ubiquitin
1060
1075
  ^^^ we want to obtain the ubuiqitin sequence
1061
1076
  --------------------------------------------------------------------------------
1062
- (172) → Telomers
1077
+ (171) → Telomers
1063
1078
  Telomeres are listed from 5' to 3'.
1064
1079
  Example for the human telomeres would be:
1065
1080
  5'-TTAGGG-3
@@ -1068,25 +1083,25 @@
1068
1083
  doc_telomeres
1069
1084
  ^^^ add this to say the human telomere sequence
1070
1085
  --------------------------------------------------------------------------------
1071
- (173) → ORF_positions?
1086
+ (172) → ORF_positions?
1072
1087
  ^^^ change this a bit, to actually show the positions
1073
1088
  of the various ORFs with the start-position.
1074
1089
  --------------------------------------------------------------------------------
1075
- (174) → add:
1090
+ (173) → add:
1076
1091
  setgene2
1077
1092
  add_dna2
1078
1093
  dna2
1079
1094
  dna? <--- this one is not a setter but a query.
1080
1095
  --------------------------------------------------------------------------------
1081
- (175) → improve the TM calculation. must be better, must have more
1096
+ (174) → improve the TM calculation. must be better, must have more
1082
1097
  documentation, and a small tutorial.
1083
1098
  --------------------------------------------------------------------------------
1084
- (176) → Compare bioroebe to:
1099
+ (175) → Compare bioroebe to:
1085
1100
  https://www.ncbi.nlm.nih.gov/orffinder
1086
1101
  whether both return the same
1087
1102
  also possibly add a web-gui
1088
1103
  --------------------------------------------------------------------------------
1089
- (177) → Find out ratios from:
1104
+ (176) → Find out ratios from:
1090
1105
  Doolittle RF. 1989. Redundancies in protein sequences. I
1091
1106
  http://onlinelibrary.wiley.com/doi/10.1110/ps.9.6.1203/pdf
1092
1107
  ^^^ that table perhaps
@@ -1105,33 +1120,33 @@
1105
1120
  Bioroebe::Blosum[50] as an API.
1106
1121
  and document it in general.
1107
1122
  --------------------------------------------------------------------------------
1108
- (178) → http://www.biomart.org/other/user-docs.pdf
1123
+ (177) → http://www.biomart.org/other/user-docs.pdf
1109
1124
  ^^^ work through this
1110
1125
  --------------------------------------------------------------------------------
1111
- (179) → add:
1126
+ (178) → add:
1112
1127
  class Cell
1113
1128
  ^^^ simulate a cell
1114
1129
  Hmmm. Needs specific components ... and needs a better plan.
1115
1130
  --------------------------------------------------------------------------------
1116
- (180) → class Protein:
1131
+ (179) → class Protein:
1117
1132
  add glycosyslation patteren
1118
1133
  .glycosylated? yes no
1119
1134
  + glycoslated?
1120
1135
  need to somehow add the modiication type
1121
1136
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358406/
1122
1137
  --------------------------------------------------------------------------------
1123
- (181) → In the BioShell we must be able to do probes - completementary
1138
+ (180) → In the BioShell we must be able to do probes - completementary
1124
1139
  to amino acids.
1125
1140
  --------------------------------------------------------------------------------
1126
- (182) → Add www-related functionality to bioroebe eventually make use
1141
+ (181) → Add www-related functionality to bioroebe eventually make use
1127
1142
  of rails, but start with sinatra possibly. In the long run,
1128
1143
  make it flexible to work with as many different frameworks
1129
1144
  as possible, though.
1130
1145
  --------------------------------------------------------------------------------
1131
- (183) → Spaltstellen anzeigen zum beispiel lambda-DNA verdau
1146
+ (182) → Spaltstellen anzeigen zum beispiel lambda-DNA verdau
1132
1147
  BgI II.
1133
1148
  --------------------------------------------------------------------------------
1134
- (184) → dnaanalyze
1149
+ (183) → dnaanalyze
1135
1150
  In the DNA string `TCCGTCGCAACACATCGCCTCAACAAACCGACCGGGATATGCAATACCGGAATCCGATCCTTTAGAAGCTGCATTCCAAACGCTTGCAATAACACCCACTCGACTATTCAGCATTGGCAAAGGGTACGAATTCGACGAAGGGAGGGTGCTATATTTTCCAAGTTGCTCGCCGATTGATACGGAGCCTGTGGAAAGATTTCGCGGCTCTAGTCTTTAGCTTTGATGTCACCCCTGAGTAGTAACCCGGCGTGGTAGCTTTCATTAGACTTCTCGGAGAGAGTATTAAGCAAAGGTGGAGGTCCCAGGGGTCCAGTGAGCTGTATCGCACTAAAAGCATGCCTACGGGCAATGCTATTTTGCTCACAGGAACTTTGGGGGAGCCACAAACTCTCGAAGCCGGATTGTTGTGGCGGCTAACTTTCCAAAGGCGACCATTCATGGTCTGAATGGGCCCTCACCAGAAGAACGTTTTCGACGGGCATTCTTCCCCGGGGTTTCGAAGGCAAGGGTCAGCACGGCGCGGAAAAGTACGCGACGCATACCGGACTAGTCATGCAACTCCCTCGGAACTGGCGATTCCCACCCAAGAGACGCACGCTGATCATTGCCCATGCCGACTGGAGATGCTGAATTTGGTATGCGGGTCTGTTGCCAGCGCTGACATTATCGGACATTGTGGGGAGAACCGTGTGATTGATTGAGCTGGCGCATTTGTCCGCATGCTCTCCTCATGTGGACACCTTCGCAGGTTCTTTCCGCGGCCACAGTGTCGGGATCTACCCCTGGTGCGTCGCCGCGAGTACAGGTGGGGTTTCGCGCATGAGAACCAATGTTGCACGCCTCAAAACATGGCTGTAACATATTAGCGCCAATAAAAATTTTTGGCAACAAAGAAACAAGGCCAACCGAAGTGCTAAGCCGCGATCATGAAGGGGCGATGCCAGAATGGGAGTCTGCCTTTCCTGTGTGGACGTGAGATTGTACCTAGACAGAGAACGCC` we found these Nucleotides:
1136
1151
  ================================================================================
1137
1152
  Adenines: 244 | 24.40 %
@@ -1150,11 +1165,11 @@
1150
1165
  can be assigned, and dnaanalyse --GUI should
1151
1166
  start it too. ALSO document it once this works.
1152
1167
  --------------------------------------------------------------------------------
1153
- (185) → go through the individual components slowly and improve them,
1168
+ (184) → go through the individual components slowly and improve them,
1154
1169
  step by step, including the documentation. Then eventually
1155
1170
  remove this todo-entry here.
1156
1171
  --------------------------------------------------------------------------------
1157
- (186) → Add a consensus sequence for:
1172
+ (185) → Add a consensus sequence for:
1158
1173
  Asn-X-Ser/Thr-Conesnsus
1159
1174
  first in a yaml file; also documented, then also add
1160
1175
  a way to scan for these something like:
@@ -1164,7 +1179,7 @@
1164
1179
  /N-?Glyc/i
1165
1180
  ^^^ use that regex
1166
1181
  --------------------------------------------------------------------------------
1167
- (187) → require 'bio'
1182
+ (186) → require 'bio'
1168
1183
  # creating a Bio::Sequence::NA object containing ambiguous alphabets
1169
1184
  ambiguous_seq = Bio::Sequence::NA.new("atgcyrwskmbdhvn")
1170
1185
  # show the contents and class of the DNA sequence object
@@ -1181,31 +1196,31 @@
1181
1196
  so taht it can be used by both the .cgi and
1182
1197
  well rdoc...
1183
1198
  --------------------------------------------------------------------------------
1184
- (188) → Add more protein-specific thingies to bioroebe.
1199
+ (187) → Add more protein-specific thingies to bioroebe.
1185
1200
  --------------------------------------------------------------------------------
1186
- (189) → Die bioshell vorantreiben und durch std_biology.rb abarbeiten.
1201
+ (188) → Die bioshell vorantreiben und durch std_biology.rb abarbeiten.
1187
1202
  Vielleicht können wir ja etwas davon auslagern in eine Klasse
1188
1203
  oder so.
1189
1204
  Das ganze sollte auch mit Webmin (biomin) verknüpft werden, so das
1190
1205
  wir die Bioshell auch elegant über das www verwenden können!
1191
1206
  --------------------------------------------------------------------------------
1192
- (190) → ^^^ when we find restriction enzyme sites in a DNA
1207
+ (189) → ^^^ when we find restriction enzyme sites in a DNA
1193
1208
  string, colourize them RED.
1194
1209
  also set it to
1195
1210
  set_restriction_size()
1196
1211
  --------------------------------------------------------------------------------
1197
- (191) → also ... while learning C++ we extend the project here...
1212
+ (190) → also ... while learning C++ we extend the project here...
1198
1213
  Useful C++ things will be combined.
1199
1214
  --------------------------------------------------------------------------------
1200
- (192) → As of April 2003, there were 176,890 total taxa represented.
1215
+ (191) → As of April 2003, there were 176,890 total taxa represented.
1201
1216
  ^^^ we need a way to also output how many entries we
1202
1217
  have there.
1203
1218
  --------------------------------------------------------------------------------
1204
- (193) → Replace bioruby with bioroebe completely!
1219
+ (192) → Replace bioruby with bioroebe completely!
1205
1220
  In order for this to work, we first need to find out
1206
1221
  what bioruby is able to do. :P
1207
1222
  --------------------------------------------------------------------------------
1208
- (194) → append 33
1223
+ (193) → append 33
1209
1224
  # ^^^ in the bioshell
1210
1225
  Only numbers were given: Adding 33 random nucleotides to the main string next.
1211
1226
  Traceback (most recent call last):
@@ -1223,7 +1238,7 @@
1223
1238
  Did you mean? return_random_codon_sequence_for_this_aminoacid_sequence
1224
1239
  ^^^^^ BUG!
1225
1240
  --------------------------------------------------------------------------------
1226
- (195) → > rest?
1241
+ (194) → > rest?
1227
1242
  We found these restriction sites within the sequence `TTCAGAACTCAACGCCTGGTTGGCCGTCCAGTAAGCTGACTAAGTAAGTCTATGCCCGCGATAACCAGGATACAGATATCGTGAAACCTGGTTTATCTCCTTCTATAAGAGTCTGCACATCTAGC`:
1228
1243
  AccII → CGCG ( 1 times found)
1229
1244
  AluI → AGCT ( 1 times found)
@@ -1233,22 +1248,22 @@
1233
1248
  BshFI → GGCC ( 1 times found)
1234
1249
  BstFNI → CGCG ( 1 times found)
1235
1250
  BstUI → CGCG ( 1 times found)
1236
- BsuRI -> GGCC ( 1 times found)
1237
- CviRI -> TGCA ( 1 times found)
1238
- Eco32I -> GATATC ( 1 times found)
1239
- EcoRV -> GATATC ( 1 times found)
1240
- FnuDII -> CGCG ( 1 times found)
1241
- HaeIII -> GGCC ( 1 times found)
1242
- HpyCH4V -> TGCA ( 1 times found)
1243
- MaeI -> CTAG ( 1 times found)
1244
- MvnI -> CGCG ( 1 times found)
1245
- PalI -> GGCC ( 1 times found)
1246
- SelI -> CGCG ( 1 times found)
1247
- ThaI -> CGCG ( 1 times found)
1251
+ BsuRI → GGCC ( 1 times found)
1252
+ CviRI → TGCA ( 1 times found)
1253
+ Eco32I → GATATC ( 1 times found)
1254
+ EcoRV → GATATC ( 1 times found)
1255
+ FnuDII → CGCG ( 1 times found)
1256
+ HaeIII → GGCC ( 1 times found)
1257
+ HpyCH4V → TGCA ( 1 times found)
1258
+ MaeI → CTAG ( 1 times found)
1259
+ MvnI → CGCG ( 1 times found)
1260
+ PalI → GGCC ( 1 times found)
1261
+ SelI → CGCG ( 1 times found)
1262
+ ThaI → CGCG ( 1 times found)
1248
1263
  XspI → CTAG ( 1 times found)
1249
1264
  ^^^^ also show the position
1250
1265
  --------------------------------------------------------------------------------
1251
- (196) → PMID entries are:
1266
+ (195) → PMID entries are:
1252
1267
  x = 'Goldman, JM, Melo JV 2003 NEJM 349:1451 14534339
1253
1268
  Lewis GD 1993 Cancer Immunol Immun other 37: 255 8102322
1254
1269
  McShane LM 2009 Clin Canc Res 15: 1898 19276274
@@ -1303,13 +1318,13 @@
1303
1318
  ^^^ enable this... but I am not sure what is meant with
1304
1319
  that. :\
1305
1320
  --------------------------------------------------------------------------------
1306
- (197) → Bei der Datenbanksuche werden die gemessenen Massen mit den Peptidmassen
1321
+ (196) → Bei der Datenbanksuche werden die gemessenen Massen mit den Peptidmassen
1307
1322
  aller Proteine bzw. Gene in einer Datenbank (NCBI, Uniprot) verglichen. DNA-
1308
1323
  Sequenzen werden dazu in Proteinsequenzen übersetzt und in silico mit der beim
1309
1324
  Verdau benutzten Protease geschnitten.
1310
1325
  ^^^ enable digestions
1311
1326
  --------------------------------------------------------------------------------
1312
- (198) → Complexity of libraries:
1327
+ (197) → Complexity of libraries:
1313
1328
  How many independent clones are necessary to represent a genome (plant,
1314
1329
  animal/fungus) or how many such clones have to be screened to have realistic
1315
1330
  chance of finding the gene of interest?
@@ -1339,7 +1354,7 @@
1339
1354
  Most plants have reasonable genome size (e.g. tomato about 800 Mb) - 15 filters
1340
1355
  have to be hybridized.
1341
1356
  --------------------------------------------------------------------------------
1342
- (199) → BIO SHELL> BglI?
1357
+ (198) → BIO SHELL> BglI?
1343
1358
  We have found a restriction enzyme called BglI.
1344
1359
  The sequence this 11-cutter relates to is: `5' - GCCNNNNNGGC - 3'`
1345
1360
  It will specifically cut between: 5' - GCCNNNN|NGGC - 3'
@@ -1368,12 +1383,12 @@
1368
1383
  List all enzymes that produce compatible ends for the enzyme.
1369
1384
  http://biopython.org/DIST/docs/api/Bio.Restriction.Restriction.Blunt-class.html
1370
1385
  --------------------------------------------------------------------------------
1371
- (200) → https://www.reddit.com/r/bioinformatics/comments/5o3kn8/bioinformatics_contest_2017_jan_23rd29th_solve_as/
1386
+ (199) → https://www.reddit.com/r/bioinformatics/comments/5o3kn8/bioinformatics_contest_2017_jan_23rd29th_solve_as/
1372
1387
  --------------------------------------------------------------------------------
1373
- (201) → Finish all of biophp integration into bioroebe.
1388
+ (200) → Finish all of biophp integration into bioroebe.
1374
1389
  http://www.biophp.org/
1375
1390
  --------------------------------------------------------------------------------
1376
- (202) → locate oriC here:
1391
+ (201) → locate oriC here:
1377
1392
  ttcgttaagtaacttcactgcccgtagtgtaccggcattcgctagcaagagtctttctg
1378
1393
  ggcaagcttcacttgtgatcgcggcctgtgcccccggaatgaaacaaccacgtccctgct
1379
1394
  aacaacgacgggaaaagggaagtgatccgtcggcagacccagactagtgcccttctccgg
@@ -1394,17 +1409,17 @@
1394
1409
  ^^^ these give us slices
1395
1410
  But I do not know how to locate ORIs.
1396
1411
  --------------------------------------------------------------------------------
1397
- (203) → ^^^ also integrate git into bioroebe.
1412
+ (202) → ^^^ also integrate git into bioroebe.
1398
1413
  --------------------------------------------------------------------------------
1399
- (204) → WIR MÜSSEN DAS HIER EXTREM VERBESSERN.
1414
+ (203) → WIR MÜSSEN DAS HIER EXTREM VERBESSERN.
1400
1415
  DANN UPLOADEN UND ALS BASIS FÜR APPLICATIONS NUTZEN.
1401
1416
  --------------------------------------------------------------------------------
1402
- (205) → Study MetaCyc
1417
+ (204) → Study MetaCyc
1403
1418
  ^^^ study metabolic pathways.
1404
1419
  http://metacyc.org/
1405
1420
  → Create KuroMetaCyc, in Analogy towards Metabolic Cycle.
1406
1421
  --------------------------------------------------------------------------------
1407
- (206) → Welcome to BioShell May 2012. Type "help" to get some help.
1422
+ (205) → Welcome to BioShell May 2012. Type "help" to get some help.
1408
1423
  Hello and welcome to the Bio Shell Version, last updated: May 2012
1409
1424
  BIO SHELL> IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI
1410
1425
  BIO SHELL> HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA
@@ -1418,7 +1433,7 @@
1418
1433
  When we type this, we then ask:
1419
1434
  "Please input your FASTA format now:"
1420
1435
  --------------------------------------------------------------------------------
1421
- (207) → http://biopython.org/DIST/docs/cookbook/Restriction.html#mozTocId101269
1436
+ (206) → http://biopython.org/DIST/docs/cookbook/Restriction.html#mozTocId101269
1422
1437
  ^^^ support this also:
1423
1438
  >>> from Bio import Restriction
1424
1439
  >>> dir()
@@ -1474,15 +1489,15 @@
1474
1489
  test.xmd
1475
1490
  /home/kumar/Desktop/test_exit/InputMicrographs/
1476
1491
  --------------------------------------------------------------------------------
1477
- (208) → BioTodo - GENESIS, science fiction.
1492
+ (207) → BioTodo - GENESIS, science fiction.
1478
1493
  - create virus(:which_one, :amount) # Note the difference to the below
1479
1494
  - create hydra(:amount)
1480
1495
  - create bread
1481
1496
  --------------------------------------------------------------------------------
1482
- (209) → both
1497
+ (208) → both
1483
1498
  ^ should work, does not work right now.
1484
1499
  --------------------------------------------------------------------------------
1485
- (210) → Taxonomy is now integrated into bioroebe. This is good but we need more
1500
+ (209) → Taxonomy is now integrated into bioroebe. This is good but we need more
1486
1501
  documentation, some more tests, a rethinking of the layout and the
1487
1502
  structures, and a fixing of the query-part of the database.
1488
1503
  Also, make sure that it does the main functions.
@@ -1494,12 +1509,12 @@
1494
1509
  AND document this related-problems too
1495
1510
  Integrate this some other day...
1496
1511
  --------------------------------------------------------------------------------
1497
- (211) → http://www.restrictionmapper.org/cgi-bin/sitefind3.pl
1512
+ (210) → http://www.restrictionmapper.org/cgi-bin/sitefind3.pl
1498
1513
  ^^^ Das sollte man integrieren, die Funktionalität, so das
1499
1514
  man ALLE Restriktion-Enzymes ausprobiert ausgehend von
1500
1515
  einer bestimmten Sequenz.
1501
1516
  --------------------------------------------------------------------------------
1502
- (212) → A search is essentially substring search across a database of strings
1517
+ (211) → A search is essentially substring search across a database of strings
1503
1518
  (albeit with a smaller alphabet). Some common use cases: one,
1504
1519
  scientists will search for certain genes that they've used in engineered
1505
1520
  plasmids. Two, since multiple codons can translate to the same amino
@@ -1515,13 +1530,13 @@
1515
1530
  Bioroebe::DetermineOptimalCodons
1516
1531
  ^^^ this is currently incomplete.
1517
1532
  --------------------------------------------------------------------------------
1518
- (213) → Redo restrictions enzymes completely.
1533
+ (212) → Redo restrictions enzymes completely.
1519
1534
  And polish this a LOT.
1520
1535
  This may take some days. But we want this to be REALLY good and
1521
1536
  lasting for a long time.
1522
1537
  Need to keep on working at that!
1523
1538
  --------------------------------------------------------------------------------
1524
- (214) → Add: average_aminoacid_weight?
1539
+ (213) → Add: average_aminoacid_weight?
1525
1540
  → === LV-Nummer 300214 UE Übung III B Sequenzanalysen in der Molekularbiologie
1526
1541
  → Pubmed
1527
1542
  → Finding sequences
@@ -1556,7 +1571,7 @@
1556
1571
  But where is the alignment comparer? perhaps hamming distance?
1557
1572
  hmm we have to see.
1558
1573
  --------------------------------------------------------------------------------
1559
- (215) → /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/menu.rb:311:in `menu': undefined method `upcase' for ["EcoRI"]:Array (NoMethodError)
1574
+ (214) → /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/menu.rb:311:in `menu': undefined method `upcase' for ["EcoRI"]:Array (NoMethodError)
1560
1575
  from /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/user_input.rb:31:in `block in enter_main_loop'
1561
1576
  from /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/user_input.rb:12:in `loop'
1562
1577
  from /Programs/Ruby/2.3.1/lib/ruby/site_ruby/2.3.0/bioroebe/bioshell/user_input.rb:12:in `enter_main_loop'
@@ -1578,10 +1593,10 @@
1578
1593
  at this date.'
1579
1594
  SendEmail.new to: Roebe.email?, data
1580
1595
  --------------------------------------------------------------------------------
1581
- (216) → Document which parts of emboss have already been copied.
1596
+ (215) → Document which parts of emboss have already been copied.
1582
1597
  → EMBOSS.md
1583
1598
  --------------------------------------------------------------------------------
1584
- (217) → Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta
1599
+ (216) → Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta
1585
1600
  Bioroebe::Shell: Now loading from `Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta`.
1586
1601
  Bioroebe::ParseFasta: Will read from the file `Trametes_versicolor_FP-101664_SS1_pyranose_2-oxidase_partial_mRNA_XM_008046051.1.fasta`.
1587
1602
  This sequence is assumed to be DNA or RNA.
@@ -1622,7 +1637,7 @@
1622
1637
  - Learn from:
1623
1638
  http://www.snapgene.com/products/snapgene_viewer/
1624
1639
  --------------------------------------------------------------------------------
1625
- (218) → Wir sollten GFP tagging unterstützen, also wie das
1640
+ (217) → Wir sollten GFP tagging unterstützen, also wie das
1626
1641
  Protein-Konstrukt aussehen soll und so weiter.
1627
1642
  Das geht teilweise...
1628
1643
  GFP? zeigt die Sequenz an.
@@ -1631,21 +1646,21 @@
1631
1646
  Was fehlt? Hmmmm... eventuell noch mehr an
1632
1647
  dokumentation.
1633
1648
  --------------------------------------------------------------------------------
1634
- (219) → in bioroebe, create subsequences for siRNA, then scan for
1649
+ (218) → in bioroebe, create subsequences for siRNA, then scan for
1635
1650
  submatcher + report where these are. Should be fast too.
1636
1651
  --------------------------------------------------------------------------------
1637
- (220) → Reverse complement now works quite well, also via the sinatra
1652
+ (219) → Reverse complement now works quite well, also via the sinatra
1638
1653
  interface. We still should have a way to show 5' and
1639
1654
  3', both on the commandline, and via sinatra.
1640
1655
  Perhaps via --fancy commandline flag or so.
1641
1656
  --------------------------------------------------------------------------------
1642
- (221) → Cn3D files?
1657
+ (220) → Cn3D files?
1643
1658
  ^^^ add support for these; research what they are, too.
1644
1659
  --------------------------------------------------------------------------------
1645
- (222) → Consider adding graphviz, perhaps to the taxonomy project
1660
+ (221) → Consider adding graphviz, perhaps to the taxonomy project
1646
1661
  where we make graphs towards different nodes or so...
1647
1662
  --------------------------------------------------------------------------------
1648
- (223) → in parse fasta
1663
+ (222) → in parse fasta
1649
1664
  @colourize_sequence = false
1650
1665
  ^^^ change this lateron...
1651
1666
  perhaps create a toplevel method
@@ -1653,7 +1668,7 @@
1653
1668
  the check better whether it is a protein or a DNA/RNA
1654
1669
  add a toplevel method for this.
1655
1670
  --------------------------------------------------------------------------------
1656
- (224) → clone the BLast ident matcher functionality for aminacids into
1671
+ (223) → clone the BLast ident matcher functionality for aminacids into
1657
1672
  Bioroebe.
1658
1673
  - fasta_download AAC76198.2
1659
1674
  ^^^ enable the above in the bioshell, and perhaps also outside
@@ -1661,7 +1676,7 @@
1661
1676
  http://www.ncbi.nlm.nih.gov/protein/145693187?report=fasta
1662
1677
  ^^^ shall use something such as the above
1663
1678
  --------------------------------------------------------------------------------
1664
- (225) → Be able to mark exon/intron boundaries.
1679
+ (224) → Be able to mark exon/intron boundaries.
1665
1680
  - Add "taxid?" to tell us the name of the organism. This works now.
1666
1681
  ^^^ should also work with a local database. ← we integrate this
1667
1682
  at a later point.
@@ -1693,15 +1708,15 @@
1693
1708
  ^^^
1694
1709
  study sumoplot ...
1695
1710
  --------------------------------------------------------------------------------
1696
- (226) → http://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/src/chapter7.html
1711
+ (225) → http://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/src/chapter7.html
1697
1712
  --------------------------------------------------------------------------------
1698
- (227) → http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc22
1713
+ (226) → http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc22
1699
1714
  ^^^ continue here; "You can also specify the table using the
1700
1715
  NCBI table number which is shorter, and often included in
1701
1716
  the feature annotation of GenBank files:"
1702
1717
  ^^^ work through this and see if it is good.
1703
1718
  --------------------------------------------------------------------------------
1704
- (228) → Clone ALL of biophp, if it us useful.
1719
+ (227) → Clone ALL of biophp, if it us useful.
1705
1720
  Then state so too, then get rid of this entry here.
1706
1721
  But remember, we must also be able to do so via a webinterface!
1707
1722
  Oligos now work. Hmm.
@@ -1734,7 +1749,7 @@
1734
1749
  We should also put this poart into doc/ subsection
1735
1750
  to keep track of what is missing and what is not.
1736
1751
  --------------------------------------------------------------------------------
1737
- (229) → sizeseq
1752
+ (228) → sizeseq
1738
1753
  ^^^ clone this functionality and describe it in detail.
1739
1754
  also for the www. Hmmm. Need to add this for the
1740
1755
  www.
@@ -1764,7 +1779,7 @@
1764
1779
  ^^^ demonstrate via foobar.fasta
1765
1780
  ALSO ADD A GUI; sizeseq.rb was added in February 2021.
1766
1781
  --------------------------------------------------------------------------------
1767
- (230) → In the sinatra-web-interface for Bioroebe:
1782
+ (229) → In the sinatra-web-interface for Bioroebe:
1768
1783
  continue quiz in rosalind !!!
1769
1784
  also, at to_dna: default to RNA
1770
1785
  And improve the general quality.
@@ -1783,9 +1798,9 @@
1783
1798
  111^^^^ in ncbi format
1784
1799
  and document all of this.
1785
1800
  --------------------------------------------------------------------------------
1786
- (231) →
1801
+ (230) →
1787
1802
  --------------------------------------------------------------------------------
1788
- (232) → Add a ruby-GUI stuff, probably the old biology/ subsection
1803
+ (231) → Add a ruby-GUI stuff, probably the old biology/ subsection
1789
1804
  will be moved into the project.
1790
1805
  Also tell how to start or get this GUI stuff to run, then add
1791
1806
  components that can be a part of bioroebe into it.
@@ -1795,7 +1810,7 @@
1795
1810
  ^^^ implement smith waterman alignment
1796
1811
  swalign AAGGGGAGGACGATGCGGATGTTC AGGGAGGACGATGCGG
1797
1812
  --------------------------------------------------------------------------------
1798
- (233) → Query: cmdline (16 nt)
1813
+ (232) → Query: cmdline (16 nt)
1799
1814
  Ref : cmdline (24 nt)
1800
1815
  Query: 1 A-GGGAGGACGATGCGG 16
1801
1816
  | |||||||||||||||
@@ -1805,7 +1820,7 @@
1805
1820
  Mismatches: 1
1806
1821
  CIGAR: 1M1D15M
1807
1822
  --------------------------------------------------------------------------------
1808
- (234) → ^^^^ also add this commandline tool
1823
+ (233) → ^^^^ also add this commandline tool
1809
1824
  bin/swalin
1810
1825
  should have same output
1811
1826
  - Gene finding in genomes
@@ -1841,7 +1856,7 @@
1841
1856
  puts seq1.to_fasta("testseq", 60)
1842
1857
  ^^^^ enable this
1843
1858
  --------------------------------------------------------------------------------
1844
- (235) → Identifying amino acid cleavage sites (Sigcleave)
1859
+ (234) → Identifying amino acid cleavage sites (Sigcleave)
1845
1860
  For amino acid sequences we may be interested to know whether
1846
1861
  the amino acid sequence contains a cleavable signal sequence
1847
1862
  for directing the transport of the protein within the cell.
@@ -1860,15 +1875,15 @@
1860
1875
  to the output of the original sigcleave utility.
1861
1876
  The syntax for using Sigcleave is as follows:
1862
1877
  # create a Seq object, for example:
1863
- $seqobj = Bio::Seq->new(-seq => "AALLHHHHHHGGGGPPRTTTTTVVVVVVVVVVVVVVV");
1878
+ $seqobj = Bio::Seq→new(-seq => "AALLHHHHHHGGGGPPRTTTTTVVVVVVVVVVVVVVV");
1864
1879
  use Bio::Tools::Sigcleave;
1865
1880
  $sigcleave_object = new Bio::Tools::Sigcleave
1866
1881
  ( -seq => $seqobj,
1867
1882
  -threshold => 3.5,
1868
1883
  -description => 'test sigcleave protein seq',
1869
1884
  );
1870
- %raw_results = $sigcleave_object->signals;
1871
- $formatted_output = $sigcleave_object->pretty_print;
1885
+ %raw_results = $sigcleave_object→signals;
1886
+ $formatted_output = $sigcleave_object→pretty_print;
1872
1887
  Please see Bio::Tools::Sigcleave for details.
1873
1888
  ^^^ add this
1874
1889
  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/Sigcleave.html
@@ -1891,15 +1906,15 @@
1891
1906
  Which one specifically? Let's see...
1892
1907
  https://www.expasy.org/
1893
1908
  --------------------------------------------------------------------------------
1894
- (236) → https://biopython.org/wiki/Category%3ACookbook
1909
+ (235) → https://biopython.org/wiki/Category%3ACookbook
1895
1910
  ^^^ clone that
1896
1911
  --------------------------------------------------------------------------------
1897
- (237) → include covid genome, and begin to analyse it in bioroebe
1912
+ (236) → include covid genome, and begin to analyse it in bioroebe
1898
1913
  "Das Genom von SARS-CoV-2 sei doppelt so groß wie jenes
1899
1914
  von Influenzaviren, daher scheinen letztere viermal
1900
1915
  so schnell zu mutieren, schrieb Moshiri."
1901
1916
  --------------------------------------------------------------------------------
1902
- (238) → Look at the GUIs that are part of the BioRoebe project.
1917
+ (237) → Look at the GUIs that are part of the BioRoebe project.
1903
1918
  Polish these part, at the least one widget, then
1904
1919
  make a screenshot, as the first one.
1905
1920
  Then upload the image + new release and docu!
@@ -1911,14 +1926,14 @@
1911
1926
  Hmmm. And then, also consider transitioning into gtk3,
1912
1927
  and make mroe screenshots.
1913
1928
  --------------------------------------------------------------------------------
1914
- (239) → https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/
1929
+ (238) → https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/
1915
1930
  http://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=emboss_pepstats-I20160208-020243-0564-53154194-oy
1916
1931
  ^^^^ clone the pepstat functionality
1917
1932
  printAA RLAVQYAPLSGCHSTIREDVHNLHFCRARKE*
1918
1933
  - Improve on temperature content and how it is calculated
1919
1934
  someone googled for it in 2014 so build on it
1920
1935
  --------------------------------------------------------------------------------
1921
- (240) → pfasta /Depot/Temp/bioroebe/NM_000539.3_Homo_sapiens_rhodopsin_RHO.fasta
1936
+ (239) → pfasta /Depot/Temp/bioroebe/NM_000539.3_Homo_sapiens_rhodopsin_RHO.fasta
1922
1937
  Will read from the file `/Depot/Temp/bioroebe/NM_000539.3_Homo_sapiens_rhodopsin_RHO.fasta`.
1923
1938
  Bioroebe::ParseFasta: This sequence is assumed to be a protein.
1924
1939
  This sequence has 2768 aminoacids.
@@ -1928,7 +1943,7 @@
1928
1943
  AGAGTCATCCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAG
1929
1944
  AGAGTCATCCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAG
1930
1945
  --------------------------------------------------------------------------------
1931
- (241) → Formats
1946
+ (240) → Formats
1932
1947
  BioPerl's SeqIO system understands lot of formats and can interconvert
1933
1948
  all of them. Here is a current listing of formats, as of version 1.6.
1934
1949
  ^^^ must implement this too
@@ -1976,10 +1991,10 @@
1976
1991
  tinyseq NCBI TinySeq XML
1977
1992
  ztr ZTR tracefile ztr
1978
1993
  --------------------------------------------------------------------------------
1979
- (242) → Look at f1 display:
1994
+ (241) → Look at f1 display:
1980
1995
  10 20 30 40 50 60 70 80 90 100
1981
1996
  --------------------------------------------------------------------------------
1982
- (243) → 1 ATGCAGTTACTTCGCTGTTTTTCAATATTTTCTGTTATTGCTTCAGTTTTAGCACAGGAACTGACAACTATATGCGAGCAAATCCCCTCACCAACTTTAG 100
1997
+ (242) → 1 ATGCAGTTACTTCGCTGTTTTTCAATATTTTCTGTTATTGCTTCAGTTTTAGCACAGGAACTGACAACTATATGCGAGCAAATCCCCTCACCAACTTTAG 100
1983
1998
  F1 1 M Q L L R C F S I F S V I A S V L A Q E L T T I C E Q I P S P T L E 34
1984
1999
  ^^^ when we do f1
1985
2000
  the aminoacid sequence position is on the next
@@ -1991,7 +2006,7 @@
1991
2006
  BEFORE we add ANY COLOURS.
1992
2007
  OH WELL.
1993
2008
  --------------------------------------------------------------------------------
1994
- (244) → Add a primer-design widget
2009
+ (243) → Add a primer-design widget
1995
2010
  The idea is to be able to manipulate forward and
1996
2011
  reverse primer areas.
1997
2012
  AND research how to do this ...
@@ -2001,7 +2016,7 @@
2001
2016
  ^^^ and check what is useful there. perhaps also add
2002
2017
  nicer visual cues to pretty it up a bit.
2003
2018
  --------------------------------------------------------------------------------
2004
- (245) → Compare bioroebe to:
2019
+ (244) → Compare bioroebe to:
2005
2020
  https://www.ncbi.nlm.nih.gov/orffinder
2006
2021
  whether both return the same also possibly add a web-gui
2007
2022
  → it must also allow for different tables to be used!
@@ -2009,18 +2024,18 @@
2009
2024
  but also in different ORFs
2010
2025
  und die länge angeben, zumindest vom längsten ORF start + stop... also so das das ergebnis auch passt
2011
2026
  --------------------------------------------------------------------------------
2012
- (246) → test reverse complement in bioroebe
2027
+ (245) → test reverse complement in bioroebe
2013
2028
  ^^^
2014
2029
  new_WWW/
2015
2030
  ^^^ this should eventually become the new web-related interface.
2016
2031
  Ah well. Perhaps not ... ruby-cgi is soooooo annoying ...
2017
2032
  --------------------------------------------------------------------------------
2018
- (247) → the blosum-viewer should be supported in the cgi part
2033
+ (246) → the blosum-viewer should be supported in the cgi part
2019
2034
  and sinatra part as well.
2020
2035
  This now works for sinatra. Need to enable this for
2021
2036
  the cgi-part too eventually.
2022
2037
  --------------------------------------------------------------------------------
2023
- (248) → port the sinatra stuff together in bioroebe
2038
+ (247) → port the sinatra stuff together in bioroebe
2024
2039
  create a dir: web_api
2025
2040
  ^^^ also make params? usable in both sinatra and cgi page
2026
2041
  well ...............
@@ -2031,47 +2046,47 @@
2031
2046
  and replace the ad-hoc code otherwise...
2032
2047
  ^^^ yeah, finish the HtmlTemplate stuff.
2033
2048
  --------------------------------------------------------------------------------
2034
- (249) → https://i.imgur.com/ptcSn12.png
2049
+ (248) → https://i.imgur.com/ptcSn12.png
2035
2050
  ^^^ enable such an overview; this shows mass compuation e.g
2036
2051
  peptide mass and such
2037
2052
  --------------------------------------------------------------------------------
2038
- (250) → Bioroebe.sanitize_nucleotide_sequence
2053
+ (249) → Bioroebe.sanitize_nucleotide_sequence
2039
2054
  ^^^ port this into java. The code has been written for this already,
2040
2055
  but we currently fail to link it.
2041
2056
  --------------------------------------------------------------------------------
2042
- (251) → Batch-create the .exe files on windows for libui, once
2057
+ (250) → Batch-create the .exe files on windows for libui, once
2043
2058
  the first has been added. And then test it too
2044
2059
  AND document it. This should be done with the controller
2045
2060
  eventually. Once this works, we can remove this entry
2046
2061
  here.
2047
2062
  --------------------------------------------------------------------------------
2048
- (252) → port more libui stuff in bioroebe. We have two widgets ported so far;
2063
+ (251) → port more libui stuff in bioroebe. We have two widgets ported so far;
2049
2064
  add more such entries.
2050
2065
  --------------------------------------------------------------------------------
2051
- (253) → after libui has been ported, explore how gosu works on windows.
2066
+ (252) → after libui has been ported, explore how gosu works on windows.
2052
2067
  if possible add things to a gosu-specific UI as well, but
2053
2068
  we may need a common, unified GUI base for that.
2054
2069
  --------------------------------------------------------------------------------
2055
- (254) → (86)
2070
+ (253) → (86)
2056
2071
  add libui bindings AND once done make sure the controller works in
2057
2072
  libui as well. Embed the various things into it.
2058
2073
  Tab A set named tabs for placing items in
2059
2074
  ^^^ use this perhaps also in bioroebe hmmm
2060
2075
  yeah.
2061
2076
  --------------------------------------------------------------------------------
2062
- (255) → https://github.com/cnjinhao/nana/wiki/User-Works-using-Nana
2077
+ (254) → https://github.com/cnjinhao/nana/wiki/User-Works-using-Nana
2063
2078
  ^^^ port the "DNA hybrid"
2064
2079
  https://camo.githubusercontent.com/4c27d554ca4d698d288628f21255f917c2c577e35d7e11dd67e21880d56b6b0a/687474703a2f2f6e616e6170726f2e6f72672f696d616765732f73637265656e73686f74732f746864795f7365715f6578706c2e706e67
2065
2080
  --------------------------------------------------------------------------------
2066
- (256) → Bioroebe::Cell
2081
+ (255) → Bioroebe::Cell
2067
2082
  ^^^ think about what to do with it. If we don't need it then perhaps
2068
2083
  we should just remove it. Think about this more at 2022, before
2069
2084
  deciding what to do.
2070
2085
  --------------------------------------------------------------------------------
2071
- (257) → Add emboss cgplot functionality.
2086
+ (256) → Add emboss cgplot functionality.
2072
2087
  https://www.bioinformatics.nl/cgi-bin/emboss/cpgplot
2073
2088
  --------------------------------------------------------------------------------
2074
- (258) → integrate calculation of the Instability index (II)
2089
+ (257) → integrate calculation of the Instability index (II)
2075
2090
  The instability index provides an estimate of the
2076
2091
  stability of your protein in a test tube. Statistical
2077
2092
  analysis of 12 unstable and 32 stable proteins has
@@ -2096,14 +2111,14 @@
2096
2111
  The instability index (II) is computed to be 65.43
2097
2112
  This classifies the protein as unstable.
2098
2113
  --------------------------------------------------------------------------------
2099
- (259) → We have now added a method to show all hydrophobic amino acids, via the
2114
+ (258) → We have now added a method to show all hydrophobic amino acids, via the
2100
2115
  method .hydrophobic_amino_acids?. This works and has been documented
2101
2116
  in May 2022. However had, we also still need a way to PREDICT
2102
2117
  hydrophobic segments in a polypeptide sequence.
2103
2118
  --------------------------------------------------------------------------------
2104
- (260) → <img src="https://i.imgur.com/tkB8MTJ.png" style="margin: 1em">
2119
+ (259) → <img src="https://i.imgur.com/tkB8MTJ.png" style="margin: 1em">
2105
2120
  --------------------------------------------------------------------------------
2106
- (261) → https://www.studocu.com/en-us/document/queens-college-cuny/biochemistry-laboratory/bioinformatics-exercise/13329106
2121
+ (260) → https://www.studocu.com/en-us/document/queens-college-cuny/biochemistry-laboratory/bioinformatics-exercise/13329106
2107
2122
  ^^^ this enable via a method
2108
2123
  and add a screenshot
2109
2124
  we want to colourize an existing string
@@ -2115,7 +2130,7 @@
2115
2130
  However had, we should add a sinatra demo app too,
2116
2131
  and demonstrate this too and then documen it as-is
2117
2132
  --------------------------------------------------------------------------------
2118
- (262) →
2133
+ (261) →
2119
2134
  make sure we have a good fasta-showing widget
2120
2135
  show how many nucleotides are
2121
2136
  AND add support to modify this as-is
@@ -2127,7 +2142,7 @@
2127
2142
  or something ... perhaps also keybindings by default
2128
2143
  and a help option somewhere to explain all of this.
2129
2144
  --------------------------------------------------------------------------------
2130
- (263) → Add a way in bioroebe to store a gene into a yaml file
2145
+ (262) → Add a way in bioroebe to store a gene into a yaml file
2131
2146
  or so, and to also load it up again. Perhaps simplify
2132
2147
  this automatically. Need some ways to describe that.
2133
2148
  FastaToYaml
@@ -2136,55 +2151,55 @@
2136
2151
  This class now exists. We have to add more features to it
2137
2152
  eventually, though.
2138
2153
  --------------------------------------------------------------------------------
2139
- (264) → https://pubchem.ncbi.nlm.nih.gov/compound/16131099#section=Top
2154
+ (263) → https://pubchem.ncbi.nlm.nih.gov/compound/16131099#section=Top
2140
2155
  ^^^ this website is quite interesting; try to use components
2141
2156
  from it.
2142
2157
  --------------------------------------------------------------------------------
2143
- (265) → Add some option to show the aminoacid sequence, at the least
2158
+ (264) → Add some option to show the aminoacid sequence, at the least
2144
2159
  store it; and optionally show it.
2145
2160
  possibly always report how many aminoacids are
2146
2161
  part of that file; and optionally also show
2147
2162
  the whole sequence.
2148
2163
  --------------------------------------------------------------------------------
2149
- (266) → http://insilico.ehu.es/
2164
+ (265) → http://insilico.ehu.es/
2150
2165
  ^^^ check if we have all of this incorporated
2151
2166
  --------------------------------------------------------------------------------
2152
- (267) → Integrate these nice GUI parts parts:
2167
+ (266) → Integrate these nice GUI parts parts:
2153
2168
  https://dev.to/kojix2/introduction-to-gr-rb-data-visualization-with-ruby-2c39
2154
2169
  --------------------------------------------------------------------------------
2155
- (268) → AND THEN test on windows as well.
2170
+ (267) → AND THEN test on windows as well.
2156
2171
  ^^^^^^^^^^^^^^
2157
2172
  --------------------------------------------------------------------------------
2158
- (269) → add mouse chromsoome URL, also in the bioshell
2173
+ (268) → add mouse chromsoome URL, also in the bioshell
2159
2174
  and the main README, to be of help for the
2160
2175
  user. add a mouse subsection.
2161
2176
  --------------------------------------------------------------------------------
2162
- (270) → fix the taxonomy stuff...
2177
+ (269) → fix the taxonomy stuff...
2163
2178
  --------------------------------------------------------------------------------
2164
- (271) → set_dna_sequence alu
2179
+ (270) → set_dna_sequence alu
2165
2180
  ^^^ fetch random alu
2166
2181
  ^^^ alu sequence
2167
2182
  Ok we started this now adding more details, but we
2168
2183
  need to become better at searching for this
2169
2184
  sequence.
2170
2185
  --------------------------------------------------------------------------------
2171
- (272) → draw things based on GR
2186
+ (271) → draw things based on GR
2172
2187
  --------------------------------------------------------------------------------
2173
- (273) → https://mycocosm.jgi.doe.gov/help/screenshots/browser_viewer.png
2188
+ (272) → https://mycocosm.jgi.doe.gov/help/screenshots/browser_viewer.png
2174
2189
  ^^^ offer the same functionality
2175
2190
  --------------------------------------------------------------------------------
2176
- (274) → https://genome.cshlp.org/content/12/10/1611/F3.expansion.html
2191
+ (273) → https://genome.cshlp.org/content/12/10/1611/F3.expansion.html
2177
2192
  ^^^ enable this, we must obtain a sequence then store into genbank format
2178
2193
  so, first fetch; then store as-is.
2179
2194
  --------------------------------------------------------------------------------
2180
- (275) → be able to generate nice graphics
2195
+ (274) → be able to generate nice graphics
2181
2196
  https://genome.cshlp.org/content/12/10/1611/F1.large.jpg
2182
2197
  --------------------------------------------------------------------------------
2183
- (276) → add rmagicks wrappre, perhaps via imageparadise or something
2198
+ (275) → add rmagicks wrappre, perhaps via imageparadise or something
2184
2199
  the idea is that we can make fancy drawings and generate
2185
2200
  an image for the end user to see
2186
2201
  --------------------------------------------------------------------------------
2187
- (277) → https://bioperl.org/howtos/Beginners_HOWTO.html#item13
2202
+ (276) → https://bioperl.org/howtos/Beginners_HOWTO.html#item13
2188
2203
  extend the sequence object and document it
2189
2204
  also add:
2190
2205
  class Genome
@@ -2196,7 +2211,7 @@
2196
2211
  @internal_hash[:species] # return the species here
2197
2212
  end
2198
2213
  --------------------------------------------------------------------------------
2199
- (278) → http://lib.ysu.am/open_books/312400.pdf
2214
+ (277) → http://lib.ysu.am/open_books/312400.pdf
2200
2215
  clone:
2201
2216
  Primer.pl
2202
2217
  This program was written to support the required informatics for a sequencing
@@ -2219,23 +2234,23 @@
2219
2234
  of the program lie in the classes and the methods we call. The next section
2220
2235
  examines the Primer3 module, which is similar to many Bioperl modules
2221
2236
  --------------------------------------------------------------------------------
2222
- (279) → Clone all of Emboss. :)
2237
+ (278) → Clone all of Emboss. :)
2223
2238
  → Clone and document the getorf functionality properly.
2224
2239
  See: http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html
2225
2240
  http://emboss.sourceforge.net
2226
2241
  http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html
2227
2242
  --------------------------------------------------------------------------------
2228
- (280) → Add useful formulas for bioshell.
2243
+ (279) → Add useful formulas for bioshell.
2229
2244
  --------------------------------------------------------------------------------
2230
- (281) → Polish the GUI sets:
2245
+ (280) → Polish the GUI sets:
2231
2246
  https://i.imgur.com/djElIMh.png
2232
2247
  --------------------------------------------------------------------------------
2233
- (282) → The taxonomy part should be fully integrated, without it
2248
+ (281) → The taxonomy part should be fully integrated, without it
2234
2249
  being a standalone part anymore.
2235
2250
  continue on the taxonomy stuff.
2236
2251
  ne day this will work again *shake fist*
2237
2252
  --------------------------------------------------------------------------------
2238
- (283) → Show the frequency of codons in different tables
2253
+ (282) → Show the frequency of codons in different tables
2239
2254
  This works quite ok, but right now the approach is to store
2240
2255
  this in a .yml file which is not ideal.
2241
2256
  Thus, we have to add two things:
@@ -2246,14 +2261,14 @@
2246
2261
  Add where this can be found.
2247
2262
  IMPROVE THIS ALL!!!!!!!
2248
2263
  --------------------------------------------------------------------------------
2249
- (284) → improve docu + tests for melting temperature analysis again
2264
+ (283) → improve docu + tests for melting temperature analysis again
2250
2265
  + usage example + GUI + web-use
2251
2266
  --------------------------------------------------------------------------------
2252
- (285) → https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec15
2267
+ (284) → https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec15
2253
2268
  ^^^ work through the above, also integrate it + write docs
2254
2269
  https://raw.githubusercontent.com/biopython/biopython/master/Doc/examples/ls_orchid.fasta
2255
2270
  --------------------------------------------------------------------------------
2256
- (286) → work a bit more on tk!!!
2271
+ (285) → work a bit more on tk!!!
2257
2272
  in particular to start it from the bioshell as-is.
2258
2273
  ^^^ this is mostly done for quick
2259
2274
  demonstration purposes
@@ -2264,15 +2279,18 @@
2264
2279
  protein_to_DNA
2265
2280
  ^^^^ improve both while improving tk_paradise docu as well.
2266
2281
  --------------------------------------------------------------------------------
2267
- (287) → add 2nd_orf
2282
+ (286) → add 2nd_orf
2268
2283
  → this shall scan for the 2nd orf
2269
2284
  → and third ORF as well, then, and document it.
2270
2285
  --------------------------------------------------------------------------------
2271
- (288) → https://github.com/pjotrp/bigbio
2286
+ (287) → https://github.com/pjotrp/bigbio
2272
2287
  ^^^^ include uses cases from that readme
2273
2288
  --------------------------------------------------------------------------------
2274
- (289) -> bioinformatiocs bioroebe:
2275
- cut_via(:trypsin)
2276
- ^^^^ show the digest as array
2277
- then upload after documenting this
2278
- ------------------------------------------------------------------------
2289
+ (288) → bioinformatiocs bioroebe:
2290
+ cut_via(:trypsin)
2291
+ ^^^^ show the digest as array
2292
+ then upload after documenting this
2293
+ --------------------------------------------------------------------------------
2294
+ (289) -> we need to be able to draw graphical elements such as a bar
2295
+ with an arrow, representing DNA.
2296
+