bioroebe 0.10.80 → 0.11.24

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Files changed (129) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +1204 -772
  3. data/bioroebe.gemspec +3 -3
  4. data/doc/README.gen +1203 -771
  5. data/doc/todo/bioroebe_todo.md +391 -365
  6. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  7. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  8. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  9. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  10. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  11. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  12. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
  13. data/lib/bioroebe/base/commandline_application/misc.rb +18 -8
  14. data/lib/bioroebe/base/misc.rb +16 -0
  15. data/lib/bioroebe/base/prototype/misc.rb +1 -1
  16. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  17. data/lib/bioroebe/codons/show_codon_usage.rb +2 -1
  18. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  19. data/lib/bioroebe/constants/database_constants.rb +1 -1
  20. data/lib/bioroebe/constants/files_and_directories.rb +20 -1
  21. data/lib/bioroebe/constants/misc.rb +20 -0
  22. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  23. data/lib/bioroebe/crystal/README.md +2 -0
  24. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  25. data/lib/bioroebe/data/README.md +11 -8
  26. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  27. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  28. data/lib/bioroebe/{shell/tk.rb → electron_microscopy/electron_microscopy_module.rb} +15 -10
  29. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  30. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  31. data/lib/bioroebe/genome/README.md +4 -0
  32. data/lib/bioroebe/genome/genome.rb +67 -0
  33. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  34. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  35. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  36. data/lib/bioroebe/misc/ruler.rb +1 -0
  37. data/lib/bioroebe/parsers/genbank_parser.rb +353 -24
  38. data/lib/bioroebe/parsers/gff.rb +1 -9
  39. data/lib/bioroebe/pdb/parse_pdb_file.rb +1 -9
  40. data/lib/bioroebe/project/project.rb +1 -1
  41. data/lib/bioroebe/python/README.md +1 -0
  42. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  43. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  44. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  45. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  46. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  47. data/lib/bioroebe/python/mymodule.py +8 -0
  48. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  49. data/lib/bioroebe/python/shell/shell.py +19 -0
  50. data/lib/bioroebe/python/to_rna.py +14 -0
  51. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  52. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  53. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  54. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +34 -0
  55. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  56. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +11 -0
  57. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  58. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  59. data/lib/bioroebe/sequence/protein.rb +105 -3
  60. data/lib/bioroebe/sequence/sequence.rb +61 -2
  61. data/lib/bioroebe/shell/menu.rb +3451 -3366
  62. data/lib/bioroebe/shell/misc.rb +51 -4311
  63. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  64. data/lib/bioroebe/shell/shell.rb +11192 -28
  65. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  66. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  67. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  68. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  69. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  70. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  71. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  72. data/lib/bioroebe/taxonomy/info/info.rb +17 -2
  73. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  74. data/lib/bioroebe/taxonomy/interactive.rb +139 -95
  75. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  76. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  77. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  78. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  79. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  80. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  81. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +101 -63
  82. data/lib/bioroebe/toplevel_methods/misc.rb +17 -16
  83. data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
  84. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  85. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  86. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  87. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  88. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  89. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  90. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  91. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  92. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  93. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  94. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  95. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  96. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  97. data/lib/bioroebe/version/version.rb +2 -2
  98. data/lib/bioroebe/www/embeddable_interface.rb +101 -52
  99. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  100. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  101. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  102. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  103. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
  104. metadata +32 -35
  105. data/doc/setup.rb +0 -1655
  106. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  107. data/lib/bioroebe/shell/add.rb +0 -108
  108. data/lib/bioroebe/shell/assign.rb +0 -360
  109. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  110. data/lib/bioroebe/shell/constants.rb +0 -166
  111. data/lib/bioroebe/shell/download.rb +0 -335
  112. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  113. data/lib/bioroebe/shell/enzymes.rb +0 -310
  114. data/lib/bioroebe/shell/fasta.rb +0 -345
  115. data/lib/bioroebe/shell/gtk.rb +0 -76
  116. data/lib/bioroebe/shell/history.rb +0 -132
  117. data/lib/bioroebe/shell/initialize.rb +0 -217
  118. data/lib/bioroebe/shell/loop.rb +0 -74
  119. data/lib/bioroebe/shell/prompt.rb +0 -107
  120. data/lib/bioroebe/shell/random.rb +0 -289
  121. data/lib/bioroebe/shell/reset.rb +0 -335
  122. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  123. data/lib/bioroebe/shell/search.rb +0 -337
  124. data/lib/bioroebe/shell/sequences.rb +0 -200
  125. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  126. data/lib/bioroebe/shell/startup.rb +0 -127
  127. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  128. data/lib/bioroebe/shell/user_input.rb +0 -88
  129. data/lib/bioroebe/shell/xorg.rb +0 -45
data/lib/bioroebe/sequence/sequence.rb CHANGED
@@ -188,6 +188,27 @@ class Sequence < ::Bioroebe::RawSequence
188
188
  @internal_hash[:type]
189
189
  end; alias type type? # === type
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190
 
191
+ # ========================================================================= #
192
+ # === index
193
+ # ========================================================================= #
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+ def index(i)
195
+ @sequence.index(i)
196
+ end
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+
198
+ # ========================================================================= #
199
+ # === map
200
+ # ========================================================================= #
201
+ def map(&block)
202
+ @sequence.map(&block)
203
+ end
204
+
205
+ # ========================================================================= #
206
+ # === size?
207
+ # ========================================================================= #
208
+ def size?
209
+ @sequence.size
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+ end
211
+
191
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  # ========================================================================= #
192
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  # === to_regexp
193
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  #
@@ -334,7 +355,7 @@ class Sequence < ::Bioroebe::RawSequence
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  # ===================================================================== #
335
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  sequence?.tr!('T','U') if sequence?
336
357
  end
337
- end
358
+ end; alias normalize sanitize_dataset # === normalize
338
359
 
339
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  # ========================================================================= #
340
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  # === set_type
@@ -484,7 +505,8 @@ class Sequence < ::Bioroebe::RawSequence
484
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  # ===================================================================== #
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  # === :do_not_downcase
486
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  # ===================================================================== #
487
- when :do_not_downcase
508
+ when :do_not_downcase,
509
+ :make_no_modification
488
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  # Make no modification in this case.
489
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  # ===================================================================== #
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  # === :do_upcase
@@ -526,6 +548,16 @@ class Sequence < ::Bioroebe::RawSequence
526
548
  end; alias set_rna_type set_rna # === set_rna_type
527
549
  alias convert_to_rna set_rna # === convert_to_rna
528
550
 
551
+ # ========================================================================= #
552
+ # === automatic_support_for_nucleotides
553
+ #
554
+ # This adds automatic support for RNA and DNA to this sequence object.
555
+ # ========================================================================= #
556
+ def automatic_support_for_nucleotides
557
+ require 'bioroebe/sequence/nucleotide_module/nucleotide_module.rb'
558
+ extend(Bioroebe::NucleotideModule)
559
+ end
560
+
529
561
  # ========================================================================= #
530
562
  # === set_dna
531
563
  # ========================================================================= #
@@ -544,6 +576,33 @@ class Sequence < ::Bioroebe::RawSequence
544
576
  }.join
545
577
  end
546
578
 
579
+ # ========================================================================= #
580
+ # === remove_invalid_entries_from_the_dna_sequence!
581
+ # ========================================================================= #
582
+ def remove_invalid_entries_from_the_dna_sequence!(i = sequence?)
583
+ result = i.chars.select {|character|
584
+ DNA_NUCLEOTIDES.include? character.upcase
585
+ }.join
586
+ set_sequence(result)
587
+ end
588
+
589
+ # ========================================================================= #
590
+ # === randomize
591
+ #
592
+ # Usage example:
593
+ #
594
+ # x = Bioroebe::Sequence.new; x.randomize
595
+ #
596
+ # ========================================================================= #
597
+ def randomize(
598
+ i = { 'A'=>1,'C'=>2,'G'=>3,'T'=>4 }
599
+ )
600
+ if i.is_a? Hash
601
+ i = i.map{|key, value| "#{key * value}" }.join
602
+ end
603
+ ::Bioroebe.random_dna(size?, i) # => "GGTAGGGGGGGGTAGGGGGG"
604
+ end
605
+
547
606
  # ========================================================================= #
548
607
  # === Bioroebe::Sequence.sequence_from_file
549
608
  #