bioroebe 0.10.80

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Files changed (802) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.md +428 -0
  3. data/README.md +9280 -0
  4. data/bin/advanced_dotplot +7 -0
  5. data/bin/align_open_reading_frames +12 -0
  6. data/bin/all_positions_of_this_nucleotide +7 -0
  7. data/bin/aminoacid_composition +7 -0
  8. data/bin/aminoacid_frequencies +12 -0
  9. data/bin/aminoacid_substitution +7 -0
  10. data/bin/automatically_rename_this_fasta_file +7 -0
  11. data/bin/base_composition +7 -0
  12. data/bin/batch_create_windows_executables +7 -0
  13. data/bin/biomart_console +11 -0
  14. data/bin/bioroebe +27 -0
  15. data/bin/bioroebe_controller +10 -0
  16. data/bin/bioshell +26 -0
  17. data/bin/blosum_2D_table +12 -0
  18. data/bin/calculate_n50_value +12 -0
  19. data/bin/chunked_display +12 -0
  20. data/bin/codon_frequency +9 -0
  21. data/bin/codon_to_aminoacid +30 -0
  22. data/bin/colourize_this_fasta_sequence +14 -0
  23. data/bin/compact_fasta_file +7 -0
  24. data/bin/complement +7 -0
  25. data/bin/complementary_dna_strand +12 -0
  26. data/bin/complementary_rna_strand +12 -0
  27. data/bin/compseq +7 -0
  28. data/bin/consensus_sequence +17 -0
  29. data/bin/count_AT +12 -0
  30. data/bin/count_GC +12 -0
  31. data/bin/create_random_aminoacids +7 -0
  32. data/bin/decode_this_aminoacid_sequence +20 -0
  33. data/bin/deduce_aminoacid_sequence +13 -0
  34. data/bin/deduce_most_likely_aminoacid_sequence +7 -0
  35. data/bin/display_aminoacid_table +12 -0
  36. data/bin/display_open_reading_frames +7 -0
  37. data/bin/dna_to_aminoacid_sequence +7 -0
  38. data/bin/dna_to_rna +7 -0
  39. data/bin/downcase_chunked_display +12 -0
  40. data/bin/download_this_pdb +7 -0
  41. data/bin/fasta_index +7 -0
  42. data/bin/fetch_data_from_uniprot +12 -0
  43. data/bin/filter_away_invalid_nucleotides +12 -0
  44. data/bin/find_substring +19 -0
  45. data/bin/genbank_to_fasta +7 -0
  46. data/bin/hamming_distance +12 -0
  47. data/bin/input_as_dna +12 -0
  48. data/bin/is_palindrome +13 -0
  49. data/bin/leading_five_prime +7 -0
  50. data/bin/levensthein +7 -0
  51. data/bin/longest_ORF +14 -0
  52. data/bin/longest_substring +12 -0
  53. data/bin/n_stop_codons_in_this_sequence +15 -0
  54. data/bin/open_reading_frames +14 -0
  55. data/bin/overwrite_fasta_header +7 -0
  56. data/bin/palindrome_2D_structure +7 -0
  57. data/bin/palindrome_generator +7 -0
  58. data/bin/parse_fasta +7 -0
  59. data/bin/partner_nucleotide +9 -0
  60. data/bin/possible_codons_for_this_aminoacid +12 -0
  61. data/bin/random_dna_sequence +12 -0
  62. data/bin/random_sequence +12 -0
  63. data/bin/raw_hamming_distance +12 -0
  64. data/bin/return_longest_substring_via_LCS_algorithm +7 -0
  65. data/bin/reverse_complement +7 -0
  66. data/bin/reverse_sequence +7 -0
  67. data/bin/ruler +12 -0
  68. data/bin/scan_this_input_for_startcodons +12 -0
  69. data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
  70. data/bin/show_atomic_composition +7 -0
  71. data/bin/show_codon_usage +12 -0
  72. data/bin/show_fasta_header +7 -0
  73. data/bin/show_nucleotide_sequence +7 -0
  74. data/bin/show_this_codon_table +7 -0
  75. data/bin/show_this_dna_sequence +7 -0
  76. data/bin/showorf +14 -0
  77. data/bin/simplify_fasta +7 -0
  78. data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
  79. data/bin/split_this_fasta_file_into_chromosomes +7 -0
  80. data/bin/strict_filter_away_invalid_aminoacids +7 -0
  81. data/bin/taxonomy +63 -0
  82. data/bin/three_to_one +7 -0
  83. data/bin/to_rna +7 -0
  84. data/bin/trailing_three_prime +7 -0
  85. data/bin/trypsin_digest +7 -0
  86. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
  87. data/bioroebe.gemspec +97 -0
  88. data/doc/IUPAC_aminoacids_code.md +36 -0
  89. data/doc/IUPAC_nucleotide_code.md +19 -0
  90. data/doc/README.gen +9237 -0
  91. data/doc/blosum.md +5 -0
  92. data/doc/compatibility/BIO_PHP.md +37 -0
  93. data/doc/compatibility/README.md +3 -0
  94. data/doc/compatibility/emboss.md +56 -0
  95. data/doc/extensive_usage_example.md +35 -0
  96. data/doc/german_names_for_the_aminoacids.md +27 -0
  97. data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
  98. data/doc/legacy_paths.md +9 -0
  99. data/doc/pdb_ATOM_entry.md +33 -0
  100. data/doc/quality_control/README.md +2 -0
  101. data/doc/quality_control/commandline_applications.md +13 -0
  102. data/doc/resources.md +23 -0
  103. data/doc/setup.rb +1655 -0
  104. data/doc/statistics/statistics.md +41 -0
  105. data/doc/todo/README.md +5 -0
  106. data/doc/todo/bioroebe_GUI_todo.md +15 -0
  107. data/doc/todo/bioroebe_todo.md +2823 -0
  108. data/doc/using_biomart.md +258 -0
  109. data/html/test.html +144 -0
  110. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
  111. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
  112. data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
  113. data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
  114. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
  115. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
  116. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
  117. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
  118. data/lib/bioroebe/annotations/README.md +2 -0
  119. data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
  120. data/lib/bioroebe/autoinclude.rb +7 -0
  121. data/lib/bioroebe/base/base.rb +35 -0
  122. data/lib/bioroebe/base/colours.rb +14 -0
  123. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
  124. data/lib/bioroebe/base/commandline_application/README.md +7 -0
  125. data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
  126. data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
  127. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
  128. data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
  129. data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
  130. data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
  131. data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
  132. data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
  133. data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
  134. data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
  135. data/lib/bioroebe/base/initialize.rb +18 -0
  136. data/lib/bioroebe/base/misc.rb +94 -0
  137. data/lib/bioroebe/base/namespace.rb +16 -0
  138. data/lib/bioroebe/base/prototype/README.md +12 -0
  139. data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
  140. data/lib/bioroebe/base/prototype/misc.rb +108 -0
  141. data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
  142. data/lib/bioroebe/base/prototype/prototype.rb +21 -0
  143. data/lib/bioroebe/base/prototype/reset.rb +26 -0
  144. data/lib/bioroebe/base/reset.rb +11 -0
  145. data/lib/bioroebe/biomart/LICENSE.md +27 -0
  146. data/lib/bioroebe/biomart/attribute.rb +77 -0
  147. data/lib/bioroebe/biomart/biomart.rb +227 -0
  148. data/lib/bioroebe/biomart/database.rb +128 -0
  149. data/lib/bioroebe/biomart/dataset.rb +572 -0
  150. data/lib/bioroebe/biomart/filter.rb +97 -0
  151. data/lib/bioroebe/biomart/server.rb +152 -0
  152. data/lib/bioroebe/blosum/blosum.rb +88 -0
  153. data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
  154. data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
  155. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
  156. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
  157. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
  158. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
  159. data/lib/bioroebe/cell/README.md +1 -0
  160. data/lib/bioroebe/cell/cell.rb +63 -0
  161. data/lib/bioroebe/cleave_and_digest/README.md +2 -0
  162. data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
  163. data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
  164. data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
  165. data/lib/bioroebe/codon_tables/README.md +9 -0
  166. data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
  167. data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
  168. data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
  169. data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
  170. data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
  171. data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
  172. data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
  173. data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
  174. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
  175. data/lib/bioroebe/codons/README.md +28 -0
  176. data/lib/bioroebe/codons/codon_table.rb +416 -0
  177. data/lib/bioroebe/codons/codon_tables.rb +123 -0
  178. data/lib/bioroebe/codons/codons.rb +517 -0
  179. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
  180. data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
  181. data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
  182. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
  183. data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
  184. data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
  185. data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
  186. data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
  187. data/lib/bioroebe/codons/start_codons.rb +105 -0
  188. data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
  189. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
  190. data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
  191. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
  192. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
  193. data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
  194. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
  195. data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
  196. data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
  197. data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
  198. data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
  199. data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
  200. data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
  201. data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
  202. data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
  203. data/lib/bioroebe/colours/colours.rb +119 -0
  204. data/lib/bioroebe/colours/misc_colours.rb +80 -0
  205. data/lib/bioroebe/colours/rev.rb +41 -0
  206. data/lib/bioroebe/colours/sdir.rb +21 -0
  207. data/lib/bioroebe/colours/sfancy.rb +21 -0
  208. data/lib/bioroebe/colours/sfile.rb +21 -0
  209. data/lib/bioroebe/colours/simp.rb +21 -0
  210. data/lib/bioroebe/colours/swarn.rb +29 -0
  211. data/lib/bioroebe/colours/use_colours.rb +27 -0
  212. data/lib/bioroebe/configuration/configuration.rb +114 -0
  213. data/lib/bioroebe/configuration/constants.rb +35 -0
  214. data/lib/bioroebe/constants/GUIs.rb +79 -0
  215. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
  216. data/lib/bioroebe/constants/base_directory.rb +120 -0
  217. data/lib/bioroebe/constants/carriage_return.rb +14 -0
  218. data/lib/bioroebe/constants/codon_tables.rb +77 -0
  219. data/lib/bioroebe/constants/database_constants.rb +107 -0
  220. data/lib/bioroebe/constants/files_and_directories.rb +579 -0
  221. data/lib/bioroebe/constants/misc.rb +189 -0
  222. data/lib/bioroebe/constants/newline.rb +14 -0
  223. data/lib/bioroebe/constants/nucleotides.rb +114 -0
  224. data/lib/bioroebe/constants/regex.rb +28 -0
  225. data/lib/bioroebe/constants/roebe.rb +38 -0
  226. data/lib/bioroebe/constants/row_terminator.rb +16 -0
  227. data/lib/bioroebe/constants/tabulator.rb +14 -0
  228. data/lib/bioroebe/constants/unicode.rb +12 -0
  229. data/lib/bioroebe/constants/urls.rb +50 -0
  230. data/lib/bioroebe/conversions/README.md +3 -0
  231. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
  232. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
  233. data/lib/bioroebe/count/README.md +1 -0
  234. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
  235. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
  236. data/lib/bioroebe/count/count_at.rb +39 -0
  237. data/lib/bioroebe/count/count_gc.rb +43 -0
  238. data/lib/bioroebe/css/README.md +5 -0
  239. data/lib/bioroebe/css/project.css +121 -0
  240. data/lib/bioroebe/data/README.md +10 -0
  241. data/lib/bioroebe/data/bam/README.md +1 -0
  242. data/lib/bioroebe/data/data.txt +192 -0
  243. data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
  244. data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
  245. data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
  246. data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
  247. data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
  248. data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
  249. data/lib/bioroebe/data/fasta/test.fasta +7 -0
  250. data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
  251. data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
  252. data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
  253. data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
  254. data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
  255. data/lib/bioroebe/data/genbank/standard.fasta +3 -0
  256. data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
  257. data/lib/bioroebe/data/gff/sample.gff +2 -0
  258. data/lib/bioroebe/data/gff/test_gene.gff +4 -0
  259. data/lib/bioroebe/data/gff/transcripts.gff +16 -0
  260. data/lib/bioroebe/data/gtf/README.md +1 -0
  261. data/lib/bioroebe/data/json/example_config.json +48 -0
  262. data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
  263. data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
  264. data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
  265. data/lib/bioroebe/data/phylip/README.md +11 -0
  266. data/lib/bioroebe/data/phylip/example.phylip +7 -0
  267. data/lib/bioroebe/data/svg/example.svg +301 -0
  268. data/lib/bioroebe/databases/README.md +1 -0
  269. data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
  270. data/lib/bioroebe/dotplots/README.md +5 -0
  271. data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
  272. data/lib/bioroebe/dotplots/dotplot.rb +184 -0
  273. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
  274. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
  275. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
  276. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
  277. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
  278. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
  279. data/lib/bioroebe/encoding/README.md +2 -0
  280. data/lib/bioroebe/encoding/encoding.rb +45 -0
  281. data/lib/bioroebe/enzymes/README.md +2 -0
  282. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
  283. data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
  284. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
  285. data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
  286. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
  287. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
  288. data/lib/bioroebe/exceptions/README.md +2 -0
  289. data/lib/bioroebe/exceptions/exceptions.rb +17 -0
  290. data/lib/bioroebe/ext/LICENCE.md +5 -0
  291. data/lib/bioroebe/ext/README.md +7 -0
  292. data/lib/bioroebe/ext/main.cpp +45 -0
  293. data/lib/bioroebe/ext/nucleotide.cpp +24 -0
  294. data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
  295. data/lib/bioroebe/ext/sequence +0 -0
  296. data/lib/bioroebe/ext/sequence.cpp +162 -0
  297. data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
  298. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
  299. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
  300. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
  301. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
  302. data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
  303. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
  304. data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
  305. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
  306. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
  307. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
  308. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
  309. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
  310. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
  311. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
  312. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
  313. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
  314. data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
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+
data/lib/bioroebe/databases/README.md ADDED
@@ -0,0 +1 @@
1
+ Code related to databases may be stored in this subdirectory.
data/lib/bioroebe/databases/download_taxonomy_database.rb ADDED
@@ -0,0 +1,102 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
4
+ # =========================================================================== #
5
+ # === Bioroebe::DownloadTaxonomyDatabase
6
+ #
7
+ # This file bundles download-related functionality into a small, mostly
8
+ # standalone-class. This class will download the taxonomy-database
9
+ # made available by NCBI.
10
+ # =========================================================================== #
11
+ # require 'bioroebe/databases/download_taxonomy_database.rb'
12
+ # =========================================================================== #
13
+ require 'bioroebe/base/commandline_application/commandline_application.rb'
14
+
15
+ module Bioroebe
16
+
17
+ class DownloadTaxonomyDatabase < ::Bioroebe::CommandlineApplication # === Bioroebe::DownloadTaxonomyDatabase
18
+
19
+ # ========================================================================= #
20
+ # === initialize
21
+ # ========================================================================= #
22
+ def initialize(
23
+ url = FTP_NCBI_TAXONOMY_DATABASE,
24
+ run_already = true
25
+ )
26
+ reset
27
+ set_url(url)
28
+ run if run_already
29
+ end
30
+
31
+ # ========================================================================= #
32
+ # === reset
33
+ # ========================================================================= #
34
+ def reset
35
+ super()
36
+ end
37
+
38
+ # ========================================================================= #
39
+ # === set_url
40
+ # ========================================================================= #
41
+ def set_url(i)
42
+ @url = i
43
+ end
44
+
45
+ # ========================================================================= #
46
+ # === determine_download_location
47
+ #
48
+ # Determine the instance variable @download_location here.
49
+ # ========================================================================= #
50
+ def determine_download_location
51
+ @download_location = taxonomy_download_directory?+
52
+ File.basename(@url)
53
+ end
54
+
55
+ # ========================================================================= #
56
+ # === download_location?
57
+ # ========================================================================= #
58
+ def download_location? # We will store the file here.
59
+ @download_location
60
+ end
61
+
62
+ # ========================================================================= #
63
+ # === report_that_we_have_finished_the_download
64
+ # ========================================================================= #
65
+ def report_that_we_have_finished_the_download
66
+ e "Finished downloading into `#{sdir(@download_location)}`."
67
+ end
68
+
69
+ # ========================================================================= #
70
+ # === run
71
+ # ========================================================================= #
72
+ def run
73
+ determine_download_location
74
+ this_dir = taxonomy_download_directory?
75
+ unless File.directory? this_dir
76
+ mkdir(this_dir) { :be_quiet }
77
+ cd this_dir
78
+ end
79
+ erev 'Downloading into `'+sdir(this_dir)+rev+'` next.'
80
+ esystem "wget #{@url}"
81
+ report_that_we_have_finished_the_download if be_verbose?
82
+ if is_on_roebe? # Extract it at once on my home system.
83
+ extract(File.basename(@url))
84
+ end
85
+ end
86
+
87
+ end
88
+
89
+ # =========================================================================== #
90
+ # === Bioroebe.download_taxonomy_database
91
+ # =========================================================================== #
92
+ def self.download_taxonomy_database(
93
+ i = ::Bioroebe::FTP_NCBI_TAXONOMY_DATABASE
94
+ )
95
+ DownloadTaxonomyDatabase.new(i)
96
+ end
97
+
98
+ end
99
+
100
+ if __FILE__ == $PROGRAM_NAME
101
+ Bioroebe.download_taxonomy_database
102
+ end # downloadtaxonomydatabase
data/lib/bioroebe/dotplots/README.md ADDED
@@ -0,0 +1,5 @@
1
+ This directory holds code that may be used to draw a dotplot.
2
+
3
+ For now I recommend to use the class Bioroebe::AdvancedDotplot -
4
+ it was written in August 2016 and may be better than the other
5
+ class called Bioroebe::Dotplot.