bioroebe 0.10.80 → 0.12.12

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Files changed (242) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3612 -2781
  3. data/bin/bioroebe +7 -1
  4. data/bin/bioroebe_hash +7 -0
  5. data/bin/codon_to_aminoacid +1 -0
  6. data/bioroebe.gemspec +3 -3
  7. data/doc/README.gen +3612 -2742
  8. data/doc/quality_control/commandline_applications.md +3 -3
  9. data/doc/todo/bioroebe_java_todo.md +22 -0
  10. data/doc/todo/bioroebe_todo.md +2059 -2615
  11. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  12. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  13. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  14. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  15. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  16. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  17. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +15 -11
  18. data/lib/bioroebe/base/commandline_application/misc.rb +66 -49
  19. data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
  20. data/lib/bioroebe/base/commandline_application/reset.rb +3 -2
  21. data/lib/bioroebe/base/misc.rb +35 -0
  22. data/lib/bioroebe/base/prototype/misc.rb +11 -1
  23. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
  24. data/lib/bioroebe/codons/codons.rb +1 -1
  25. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +192 -58
  26. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
  27. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  28. data/lib/bioroebe/codons/show_codon_usage.rb +15 -4
  29. data/lib/bioroebe/colours/rev.rb +4 -1
  30. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  31. data/lib/bioroebe/constants/database_constants.rb +1 -1
  32. data/lib/bioroebe/constants/files_and_directories.rb +31 -4
  33. data/lib/bioroebe/constants/misc.rb +20 -0
  34. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +58 -24
  35. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +3 -2
  36. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  37. data/lib/bioroebe/crystal/README.md +2 -0
  38. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  39. data/lib/bioroebe/data/README.md +11 -8
  40. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  41. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  42. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta +9 -0
  43. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta +8 -0
  44. data/lib/bioroebe/data/fasta/human/README.md +2 -0
  45. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
  46. data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
  47. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
  48. data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
  49. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
  50. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
  51. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  52. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +10 -3
  53. data/lib/bioroebe/enzymes/restriction_enzyme.rb +23 -1
  54. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +65 -0
  55. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
  56. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
  57. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
  58. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
  59. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1465 -7
  60. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
  61. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  62. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
  63. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
  64. data/lib/bioroebe/genome/README.md +4 -0
  65. data/lib/bioroebe/genome/genome.rb +67 -0
  66. data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
  67. data/lib/bioroebe/gui/gtk +1 -0
  68. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +73 -128
  69. data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
  70. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
  71. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +99 -21
  72. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
  73. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
  74. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  75. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  76. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +165 -0
  77. data/lib/bioroebe/gui/libui/alignment/alignment.rb +3 -1
  78. data/lib/bioroebe/gui/libui/controller/controller.rb +116 -0
  79. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +18 -2
  80. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +2 -0
  81. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
  82. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +102 -0
  83. data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +18 -16
  84. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  85. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
  86. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
  87. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
  88. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
  89. data/lib/bioroebe/images/FORWARD_PRIMER.png +0 -0
  90. data/lib/bioroebe/images/REVERSE_PRIMER.png +0 -0
  91. data/lib/bioroebe/java/README.md +4 -0
  92. data/lib/bioroebe/java/bioroebe/Sequence.java +25 -1
  93. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.class +0 -0
  94. data/lib/bioroebe/java/bioroebe/{Base.java → src/main/java/bioroebe/Base.java} +15 -2
  95. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/main/java/bioroebe/BisulfiteTreatment.class} +0 -0
  96. data/lib/bioroebe/java/bioroebe/{Codons.class → src/main/java/bioroebe/Codons.class} +0 -0
  97. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java +34 -0
  98. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.class +0 -0
  99. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java +101 -0
  100. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/main/java/bioroebe/GenerateRandomDnaSequence.class} +0 -0
  101. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/main/java/bioroebe/GenerateRandomDnaSequence.java} +8 -2
  102. data/lib/bioroebe/java/bioroebe/{IsPalindrome.class → src/main/java/bioroebe/IsPalindrome.class} +0 -0
  103. data/lib/bioroebe/java/bioroebe/{IsPalindrome.java → src/main/java/bioroebe/IsPalindrome.java} +5 -1
  104. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.class +0 -0
  105. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java +56 -0
  106. data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/main/java/bioroebe/RemoveFile.java} +10 -4
  107. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/main/java/bioroebe/RemoveNumbers.class} +0 -0
  108. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/main/java/bioroebe/RemoveNumbers.java} +1 -0
  109. data/lib/bioroebe/java/bioroebe/{ToCamelcase.class → src/main/java/bioroebe/ToCamelcase.class} +0 -0
  110. data/lib/bioroebe/java/bioroebe/{ToCamelcase.java → src/main/java/bioroebe/ToCamelcase.java} +3 -3
  111. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.class +0 -0
  112. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java +42 -0
  113. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.class +0 -0
  114. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.java +75 -0
  115. data/lib/bioroebe/misc/ruler.rb +11 -2
  116. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
  117. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
  118. data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
  119. data/lib/bioroebe/parsers/gff.rb +1 -9
  120. data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
  121. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
  122. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
  123. data/lib/bioroebe/pdb/parse_pdb_file.rb +4 -10
  124. data/lib/bioroebe/project/project.rb +1 -1
  125. data/lib/bioroebe/python/README.md +1 -0
  126. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  127. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  128. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  129. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  130. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  131. data/lib/bioroebe/python/mymodule.py +8 -0
  132. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  133. data/lib/bioroebe/python/shell/shell.py +19 -0
  134. data/lib/bioroebe/python/to_rna.py +14 -0
  135. data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
  136. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  137. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  138. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  139. data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
  140. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
  141. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  142. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
  143. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  144. data/lib/bioroebe/sequence/alignment.rb +14 -4
  145. data/lib/bioroebe/sequence/dna.rb +1 -0
  146. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  147. data/lib/bioroebe/sequence/protein.rb +105 -3
  148. data/lib/bioroebe/sequence/sequence.rb +87 -21
  149. data/lib/bioroebe/shell/menu.rb +3829 -3714
  150. data/lib/bioroebe/shell/misc.rb +59 -4307
  151. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  152. data/lib/bioroebe/shell/shell.rb +11255 -28
  153. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  154. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  155. data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
  156. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  157. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  158. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  159. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  160. data/lib/bioroebe/taxonomy/help/helpline.rb +2 -2
  161. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  162. data/lib/bioroebe/taxonomy/info/info.rb +18 -11
  163. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  164. data/lib/bioroebe/taxonomy/interactive.rb +140 -104
  165. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  166. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  167. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  168. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  169. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  170. data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
  171. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  172. data/lib/bioroebe/toplevel_methods/digest.rb +18 -8
  173. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
  174. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
  175. data/lib/bioroebe/toplevel_methods/frequencies.rb +8 -1
  176. data/lib/bioroebe/toplevel_methods/misc.rb +142 -12
  177. data/lib/bioroebe/toplevel_methods/nucleotides.rb +118 -46
  178. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  179. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  180. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  181. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  182. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  183. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  184. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  185. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  186. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +6 -6
  187. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  188. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  189. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  190. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +2 -2
  191. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  192. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  193. data/lib/bioroebe/version/version.rb +2 -2
  194. data/lib/bioroebe/www/embeddable_interface.rb +103 -54
  195. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  196. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  197. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  198. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  199. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  200. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +27 -27
  201. metadata +81 -64
  202. data/doc/setup.rb +0 -1655
  203. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
  204. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
  205. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
  206. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
  207. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
  208. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
  209. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  210. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  211. data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
  212. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  213. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
  214. data/lib/bioroebe/java/bioroebe.jar +0 -0
  215. data/lib/bioroebe/shell/add.rb +0 -108
  216. data/lib/bioroebe/shell/assign.rb +0 -360
  217. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  218. data/lib/bioroebe/shell/constants.rb +0 -166
  219. data/lib/bioroebe/shell/download.rb +0 -335
  220. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  221. data/lib/bioroebe/shell/enzymes.rb +0 -310
  222. data/lib/bioroebe/shell/fasta.rb +0 -345
  223. data/lib/bioroebe/shell/gtk.rb +0 -76
  224. data/lib/bioroebe/shell/history.rb +0 -132
  225. data/lib/bioroebe/shell/initialize.rb +0 -217
  226. data/lib/bioroebe/shell/loop.rb +0 -74
  227. data/lib/bioroebe/shell/prompt.rb +0 -107
  228. data/lib/bioroebe/shell/random.rb +0 -289
  229. data/lib/bioroebe/shell/reset.rb +0 -335
  230. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  231. data/lib/bioroebe/shell/search.rb +0 -337
  232. data/lib/bioroebe/shell/sequences.rb +0 -200
  233. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  234. data/lib/bioroebe/shell/startup.rb +0 -127
  235. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  236. data/lib/bioroebe/shell/tk.rb +0 -23
  237. data/lib/bioroebe/shell/user_input.rb +0 -88
  238. data/lib/bioroebe/shell/xorg.rb +0 -45
  239. /data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/main/java/bioroebe/BisulfiteTreatment.java} +0 -0
  240. /data/lib/bioroebe/java/bioroebe/{Esystem.class → src/main/java/bioroebe/Esystem.class} +0 -0
  241. /data/lib/bioroebe/java/bioroebe/{Esystem.java → src/main/java/bioroebe/Esystem.java} +0 -0
  242. /data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/main/java/bioroebe/RemoveFile.class} +0 -0
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bioroebe
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.10.80
4
+ version: 0.12.12
5
5
  platform: ruby
6
6
  authors:
7
7
  - Robert A. Heiler
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2022-06-24 00:00:00.000000000 Z
11
+ date: 2023-01-28 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: chemistry_paradise
@@ -94,8 +94,8 @@ dependencies:
94
94
  - - ">="
95
95
  - !ruby/object:Gem::Version
96
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  version: '0'
97
- description: "\nWelcome to the bioroebe-0.10.x release series! It is recommended to\nuse
98
- ruby 3.x for this series, as it is the most tested version of \nruby in regards
97
+ description: "\nWelcome to the bioroebe-0.11.x release series! It is recommended\nto
98
+ use ruby 3.x for this series, as it is the most tested version\nof ruby in regards
99
99
  to this project.\n\nThe bioroebe-project is a software suite focusing on bio-related\nlife
100
100
  sciences in general - in particular molecular biology, molecular\ngenetics, bioinformatics,
101
101
  biotechnology, system biology, synthetic\nbiology and related topics close to the
@@ -119,6 +119,7 @@ executables:
119
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  - biomart_console
120
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  - bioroebe
121
121
  - bioroebe_controller
122
+ - bioroebe_hash
122
123
  - bioshell
123
124
  - blosum_2D_table
124
125
  - calculate_n50_value
@@ -207,6 +208,7 @@ files:
207
208
  - bin/biomart_console
208
209
  - bin/bioroebe
209
210
  - bin/bioroebe_controller
211
+ - bin/bioroebe_hash
210
212
  - bin/bioshell
211
213
  - bin/blosum_2D_table
212
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  - bin/calculate_n50_value
@@ -294,10 +296,10 @@ files:
294
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  - doc/quality_control/README.md
295
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  - doc/quality_control/commandline_applications.md
296
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  - doc/resources.md
297
- - doc/setup.rb
298
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  - doc/statistics/statistics.md
299
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  - doc/todo/README.md
300
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  - doc/todo/bioroebe_GUI_todo.md
302
+ - doc/todo/bioroebe_java_todo.md
301
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  - doc/todo/bioroebe_todo.md
302
304
  - doc/using_biomart.md
303
305
  - html/test.html
@@ -430,13 +432,20 @@ files:
430
432
  - lib/bioroebe/count/count_amount_of_nucleotides.rb
431
433
  - lib/bioroebe/count/count_at.rb
432
434
  - lib/bioroebe/count/count_gc.rb
435
+ - lib/bioroebe/crystal/README.md
436
+ - lib/bioroebe/crystal/to_rna.cr
433
437
  - lib/bioroebe/css/README.md
434
438
  - lib/bioroebe/css/project.css
435
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  - lib/bioroebe/data/README.md
436
440
  - lib/bioroebe/data/bam/README.md
437
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  - lib/bioroebe/data/data.txt
442
+ - lib/bioroebe/data/electron_microscopy/pos_example.pos
443
+ - lib/bioroebe/data/electron_microscopy/test_particles.star
438
444
  - lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta
439
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  - lib/bioroebe/data/fasta/alu_elements.fasta
446
+ - lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta
447
+ - lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta
448
+ - lib/bioroebe/data/fasta/human/README.md
440
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  - lib/bioroebe/data/fasta/lady_slippers_orchid.fasta
441
450
  - lib/bioroebe/data/fasta/loxP.fasta
442
451
  - lib/bioroebe/data/fasta/ls_orchid.fasta
@@ -466,7 +475,9 @@ files:
466
475
  - lib/bioroebe/dotplots/advanced_dotplot.rb
467
476
  - lib/bioroebe/dotplots/dotplot.rb
468
477
  - lib/bioroebe/electron_microscopy/coordinate_analyzer.rb
478
+ - lib/bioroebe/electron_microscopy/electron_microscopy_module.rb
469
479
  - lib/bioroebe/electron_microscopy/fix_pos_file.rb
480
+ - lib/bioroebe/electron_microscopy/flipy.rb
470
481
  - lib/bioroebe/electron_microscopy/generate_em2em_file.rb
471
482
  - lib/bioroebe/electron_microscopy/parse_coordinates.rb
472
483
  - lib/bioroebe/electron_microscopy/read_file_xmd.rb
@@ -476,6 +487,7 @@ files:
476
487
  - lib/bioroebe/enzymes/README.md
477
488
  - lib/bioroebe/enzymes/has_this_restriction_enzyme.rb
478
489
  - lib/bioroebe/enzymes/restriction_enzyme.rb
490
+ - lib/bioroebe/enzymes/restriction_enzymes/statistics.rb
479
491
  - lib/bioroebe/enzymes/restriction_enzymes_file.rb
480
492
  - lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb
481
493
  - lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb
@@ -497,16 +509,10 @@ files:
497
509
  - lib/bioroebe/fasta_and_fastq/fasta_defline/README.md
498
510
  - lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb
499
511
  - lib/bioroebe/fasta_and_fastq/fasta_parser.rb
512
+ - lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb
500
513
  - lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb
501
514
  - lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb
502
- - lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb
503
- - lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb
504
- - lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb
505
- - lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb
506
515
  - lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb
507
- - lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb
508
- - lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb
509
- - lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb
510
516
  - lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb
511
517
  - lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb
512
518
  - lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb
@@ -519,12 +525,14 @@ files:
519
525
  - lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb
520
526
  - lib/bioroebe/genbank/README.md
521
527
  - lib/bioroebe/genbank/genbank_flat_file_format_generator.rb
522
- - lib/bioroebe/genbank/genbank_parser.rb
523
528
  - lib/bioroebe/gene/gene.rb
529
+ - lib/bioroebe/genome/README.md
530
+ - lib/bioroebe/genome/genome.rb
524
531
  - lib/bioroebe/genomes/genome_pattern.rb
525
532
  - lib/bioroebe/genomes/genome_retriever.rb
526
533
  - lib/bioroebe/gui/experimental/README.md
527
534
  - lib/bioroebe/gui/experimental/snapgene/snapgene.rb
535
+ - lib/bioroebe/gui/gtk
528
536
  - lib/bioroebe/gui/gtk3/README.md
529
537
  - lib/bioroebe/gui/gtk3/alignment/alignment.rb
530
538
  - lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb
@@ -561,11 +569,13 @@ files:
561
569
  - lib/bioroebe/gui/gtk3/three_to_one/title.rb
562
570
  - lib/bioroebe/gui/gtk3/www_finder/www_finder.config
563
571
  - lib/bioroebe/gui/gtk3/www_finder/www_finder.rb
572
+ - lib/bioroebe/gui/jruby/alignment/alignment.rb
564
573
  - lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb
565
574
  - lib/bioroebe/gui/libui/README.md
566
575
  - lib/bioroebe/gui/libui/alignment/alignment.rb
567
576
  - lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb
568
577
  - lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb
578
+ - lib/bioroebe/gui/libui/controller/controller.rb
569
579
  - lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb
570
580
  - lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb
571
581
  - lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb
@@ -575,6 +585,7 @@ files:
575
585
  - lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb
576
586
  - lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb
577
587
  - lib/bioroebe/gui/libui/three_to_one/three_to_one.rb
588
+ - lib/bioroebe/gui/shared_code/alignment/alignment_module.rb
578
589
  - lib/bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb
579
590
  - lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb
580
591
  - lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb
@@ -582,6 +593,10 @@ files:
582
593
  - lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb
583
594
  - lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb
584
595
  - lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb
596
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class
597
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class
598
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class
599
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java
585
600
  - lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb
586
601
  - lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb
587
602
  - lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb
@@ -592,7 +607,9 @@ files:
592
607
  - lib/bioroebe/images/BIOROEBE_NEW_LOGO.png
593
608
  - lib/bioroebe/images/BlosumMatrixViewer.png
594
609
  - lib/bioroebe/images/DnaToAminoacidWidget.png
610
+ - lib/bioroebe/images/FORWARD_PRIMER.png
595
611
  - lib/bioroebe/images/PRINTED_AMINOACID_TABLE.png
612
+ - lib/bioroebe/images/REVERSE_PRIMER.png
596
613
  - lib/bioroebe/images/class_ConvertAminoacidToDNA.png
597
614
  - lib/bioroebe/images/class_SimpleStringComparer.png
598
615
  - lib/bioroebe/images/example_of_FASTA_coloured_output.png
@@ -604,40 +621,45 @@ files:
604
621
  - lib/bioroebe/images/small_DNA_logo.png
605
622
  - lib/bioroebe/images/small_drosophila_image.png
606
623
  - lib/bioroebe/java/README.md
607
- - lib/bioroebe/java/bioroebe.jar
608
624
  - lib/bioroebe/java/bioroebe/AllInOne.class
609
625
  - lib/bioroebe/java/bioroebe/AllInOne.java
610
- - lib/bioroebe/java/bioroebe/Base.class
611
- - lib/bioroebe/java/bioroebe/Base.java
612
- - lib/bioroebe/java/bioroebe/BisulfiteTreatment.class
613
- - lib/bioroebe/java/bioroebe/BisulfiteTreatment.java
614
626
  - lib/bioroebe/java/bioroebe/Cat.class
615
- - lib/bioroebe/java/bioroebe/Codons.class
616
- - lib/bioroebe/java/bioroebe/Codons.java
617
- - lib/bioroebe/java/bioroebe/Esystem.class
618
- - lib/bioroebe/java/bioroebe/Esystem.java
619
627
  - lib/bioroebe/java/bioroebe/GUI/BaseFrame.class
620
628
  - lib/bioroebe/java/bioroebe/GUI/BaseFrame.java
621
- - lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.class
622
- - lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java
623
- - lib/bioroebe/java/bioroebe/IsPalindrome.class
624
- - lib/bioroebe/java/bioroebe/IsPalindrome.java
625
- - lib/bioroebe/java/bioroebe/PartnerNucleotide.class
626
- - lib/bioroebe/java/bioroebe/PartnerNucleotide.java
627
629
  - lib/bioroebe/java/bioroebe/README.md
628
- - lib/bioroebe/java/bioroebe/RemoveFile.class
629
- - lib/bioroebe/java/bioroebe/RemoveFile.java
630
- - lib/bioroebe/java/bioroebe/RemoveNumbers.class
631
- - lib/bioroebe/java/bioroebe/RemoveNumbers.java
632
630
  - lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class
633
631
  - lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java
634
632
  - lib/bioroebe/java/bioroebe/SaveFile.java
635
633
  - lib/bioroebe/java/bioroebe/Sequence.java
636
- - lib/bioroebe/java/bioroebe/ToCamelcase.class
637
- - lib/bioroebe/java/bioroebe/ToCamelcase.java
638
634
  - lib/bioroebe/java/bioroebe/ToplevelMethods.class
639
635
  - lib/bioroebe/java/bioroebe/ToplevelMethods.java
640
636
  - lib/bioroebe/java/bioroebe/enums/DNA.java
637
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.class
638
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.java
639
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/BisulfiteTreatment.class
640
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/BisulfiteTreatment.java
641
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.class
642
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java
643
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.class
644
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java
645
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Esystem.class
646
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Esystem.java
647
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/GenerateRandomDnaSequence.class
648
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/GenerateRandomDnaSequence.java
649
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/IsPalindrome.class
650
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/IsPalindrome.java
651
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.class
652
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java
653
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveFile.class
654
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveFile.java
655
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveNumbers.class
656
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveNumbers.java
657
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToCamelcase.class
658
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToCamelcase.java
659
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.class
660
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java
661
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.class
662
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.java
641
663
  - lib/bioroebe/matplotlib/matplotlib_generator.rb
642
664
  - lib/bioroebe/misc/quiz/README.md
643
665
  - lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb
@@ -677,6 +699,24 @@ files:
677
699
  - lib/bioroebe/project/project.rb
678
700
  - lib/bioroebe/protein_structure/alpha_helix.rb
679
701
  - lib/bioroebe/protein_structure/helical_wheel.rb
702
+ - lib/bioroebe/python/README.md
703
+ - lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc
704
+ - lib/bioroebe/python/gui/gtk3/all_in_one.css
705
+ - lib/bioroebe/python/gui/gtk3/all_in_one.py
706
+ - lib/bioroebe/python/gui/gtk3/widget1.py
707
+ - lib/bioroebe/python/gui/tkinter/all_in_one.py
708
+ - lib/bioroebe/python/mymodule.py
709
+ - lib/bioroebe/python/protein_to_dna.py
710
+ - lib/bioroebe/python/shell/shell.py
711
+ - lib/bioroebe/python/to_rna.py
712
+ - lib/bioroebe/python/toplevel_methods/esystem.py
713
+ - lib/bioroebe/python/toplevel_methods/open_in_browser.py
714
+ - lib/bioroebe/python/toplevel_methods/palindromes.py
715
+ - lib/bioroebe/python/toplevel_methods/rds.py
716
+ - lib/bioroebe/python/toplevel_methods/shuffleseq.py
717
+ - lib/bioroebe/python/toplevel_methods/three_delimiter.py
718
+ - lib/bioroebe/python/toplevel_methods/time_and_date.py
719
+ - lib/bioroebe/python/toplevel_methods/to_camelcase.py
680
720
  - lib/bioroebe/raw_sequence/README.md
681
721
  - lib/bioroebe/raw_sequence/raw_sequence.rb
682
722
  - lib/bioroebe/readline/README.md
@@ -719,41 +759,17 @@ files:
719
759
  - lib/bioroebe/sequence/protein.rb
720
760
  - lib/bioroebe/sequence/reverse_complement.rb
721
761
  - lib/bioroebe/sequence/sequence.rb
722
- - lib/bioroebe/shell/add.rb
723
- - lib/bioroebe/shell/assign.rb
724
- - lib/bioroebe/shell/chop_and_cut.rb
725
762
  - lib/bioroebe/shell/colours/colours.rb
726
763
  - lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml
727
764
  - lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml
728
765
  - lib/bioroebe/shell/configuration/upcase_nucleotides.yml
729
766
  - lib/bioroebe/shell/configuration/use_silent_startup.yml
730
- - lib/bioroebe/shell/constants.rb
731
- - lib/bioroebe/shell/download.rb
732
- - lib/bioroebe/shell/enable_and_disable.rb
733
- - lib/bioroebe/shell/enzymes.rb
734
- - lib/bioroebe/shell/fasta.rb
735
- - lib/bioroebe/shell/gtk.rb
736
767
  - lib/bioroebe/shell/help/class.rb
737
768
  - lib/bioroebe/shell/help/help.rb
738
- - lib/bioroebe/shell/history.rb
739
- - lib/bioroebe/shell/initialize.rb
740
- - lib/bioroebe/shell/loop.rb
741
769
  - lib/bioroebe/shell/menu.rb
742
770
  - lib/bioroebe/shell/misc.rb
743
- - lib/bioroebe/shell/prompt.rb
744
- - lib/bioroebe/shell/random.rb
745
771
  - lib/bioroebe/shell/readline/readline.rb
746
- - lib/bioroebe/shell/reset.rb
747
- - lib/bioroebe/shell/scan_and_parse.rb
748
- - lib/bioroebe/shell/search.rb
749
- - lib/bioroebe/shell/sequences.rb
750
772
  - lib/bioroebe/shell/shell.rb
751
- - lib/bioroebe/shell/show_report_and_display.rb
752
- - lib/bioroebe/shell/startup.rb
753
- - lib/bioroebe/shell/taxonomy.rb
754
- - lib/bioroebe/shell/tk.rb
755
- - lib/bioroebe/shell/user_input.rb
756
- - lib/bioroebe/shell/xorg.rb
757
773
  - lib/bioroebe/siRNA/README.md
758
774
  - lib/bioroebe/siRNA/siRNA.rb
759
775
  - lib/bioroebe/string_matching/README.md
@@ -796,6 +812,7 @@ files:
796
812
  - lib/bioroebe/toplevel_methods/cat.rb
797
813
  - lib/bioroebe/toplevel_methods/chunked_display.rb
798
814
  - lib/bioroebe/toplevel_methods/cliner.rb
815
+ - lib/bioroebe/toplevel_methods/colourize_related_methods.rb
799
816
  - lib/bioroebe/toplevel_methods/complement.rb
800
817
  - lib/bioroebe/toplevel_methods/convert_global_env.rb
801
818
  - lib/bioroebe/toplevel_methods/databases.rb
@@ -1025,7 +1042,7 @@ post_install_message: |2+
1025
1042
 
1026
1043
  For more documentation, have a look at:
1027
1044
 
1028
- https://www.rubydoc.info/gems/bioroebe/0.10.80
1045
+ https://www.rubydoc.info/gems/bioroebe/0.12.12
1029
1046
 
1030
1047
  rdoc_options: []
1031
1048
  require_paths:
@@ -1034,18 +1051,18 @@ required_ruby_version: !ruby/object:Gem::Requirement
1034
1051
  requirements:
1035
1052
  - - ">="
1036
1053
  - !ruby/object:Gem::Version
1037
- version: 2.5.8
1054
+ version: 2.7.6
1038
1055
  required_rubygems_version: !ruby/object:Gem::Requirement
1039
1056
  requirements:
1040
1057
  - - ">="
1041
1058
  - !ruby/object:Gem::Version
1042
- version: 3.3.16
1059
+ version: 3.4.5
1043
1060
  requirements: []
1044
- rubygems_version: 3.3.16
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+ rubygems_version: 3.4.5
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  signing_key:
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  specification_version: 4
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- summary: 'Welcome to the bioroebe-0.10.x release series! It is recommended to use
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- ruby 3.x for this series, as it is the most tested version of ruby in regards to
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+ summary: 'Welcome to the bioroebe-0.11.x release series! It is recommended to use
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+ ruby 3.x for this series, as it is the most tested version of ruby in regards to
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  this project. The bioroebe-project is a software suite focusing on bio-related
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  life sciences in general - in particular molecular biology, molecular genetics,
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  bioinformatics, biotechnology, system biology, synthetic biology and related topics