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
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: 0.11.24
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: 2022-08-03 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
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  - - ">="
95
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  - !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
@@ -294,7 +294,6 @@ 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
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- - doc/setup.rb
298
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  - doc/statistics/statistics.md
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  - doc/todo/README.md
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  - doc/todo/bioroebe_GUI_todo.md
@@ -430,11 +429,15 @@ files:
430
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  - lib/bioroebe/count/count_amount_of_nucleotides.rb
431
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  - lib/bioroebe/count/count_at.rb
432
431
  - lib/bioroebe/count/count_gc.rb
432
+ - lib/bioroebe/crystal/README.md
433
+ - lib/bioroebe/crystal/to_rna.cr
433
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  - lib/bioroebe/css/README.md
434
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  - lib/bioroebe/css/project.css
435
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  - lib/bioroebe/data/README.md
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  - lib/bioroebe/data/bam/README.md
437
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  - lib/bioroebe/data/data.txt
439
+ - lib/bioroebe/data/electron_microscopy/pos_example.pos
440
+ - lib/bioroebe/data/electron_microscopy/test_particles.star
438
441
  - lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta
439
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  - lib/bioroebe/data/fasta/alu_elements.fasta
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  - lib/bioroebe/data/fasta/lady_slippers_orchid.fasta
@@ -466,6 +469,7 @@ files:
466
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  - lib/bioroebe/dotplots/advanced_dotplot.rb
467
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  - lib/bioroebe/dotplots/dotplot.rb
468
471
  - lib/bioroebe/electron_microscopy/coordinate_analyzer.rb
472
+ - lib/bioroebe/electron_microscopy/electron_microscopy_module.rb
469
473
  - lib/bioroebe/electron_microscopy/fix_pos_file.rb
470
474
  - lib/bioroebe/electron_microscopy/generate_em2em_file.rb
471
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  - lib/bioroebe/electron_microscopy/parse_coordinates.rb
@@ -519,8 +523,9 @@ files:
519
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  - lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb
520
524
  - lib/bioroebe/genbank/README.md
521
525
  - lib/bioroebe/genbank/genbank_flat_file_format_generator.rb
522
- - lib/bioroebe/genbank/genbank_parser.rb
523
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  - lib/bioroebe/gene/gene.rb
527
+ - lib/bioroebe/genome/README.md
528
+ - lib/bioroebe/genome/genome.rb
524
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  - lib/bioroebe/genomes/genome_pattern.rb
525
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  - lib/bioroebe/genomes/genome_retriever.rb
526
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  - lib/bioroebe/gui/experimental/README.md
@@ -677,6 +682,22 @@ files:
677
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  - lib/bioroebe/project/project.rb
678
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  - lib/bioroebe/protein_structure/alpha_helix.rb
679
684
  - lib/bioroebe/protein_structure/helical_wheel.rb
685
+ - lib/bioroebe/python/README.md
686
+ - lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc
687
+ - lib/bioroebe/python/gui/gtk3/all_in_one.css
688
+ - lib/bioroebe/python/gui/gtk3/all_in_one.py
689
+ - lib/bioroebe/python/gui/gtk3/widget1.py
690
+ - lib/bioroebe/python/gui/tkinter/all_in_one.py
691
+ - lib/bioroebe/python/mymodule.py
692
+ - lib/bioroebe/python/protein_to_dna.py
693
+ - lib/bioroebe/python/shell/shell.py
694
+ - lib/bioroebe/python/to_rna.py
695
+ - lib/bioroebe/python/toplevel_methods/open_in_browser.py
696
+ - lib/bioroebe/python/toplevel_methods/palindromes.py
697
+ - lib/bioroebe/python/toplevel_methods/rds.py
698
+ - lib/bioroebe/python/toplevel_methods/three_delimiter.py
699
+ - lib/bioroebe/python/toplevel_methods/time_and_date.py
700
+ - lib/bioroebe/python/toplevel_methods/to_camelcase.py
680
701
  - lib/bioroebe/raw_sequence/README.md
681
702
  - lib/bioroebe/raw_sequence/raw_sequence.rb
682
703
  - lib/bioroebe/readline/README.md
@@ -719,41 +740,17 @@ files:
719
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  - lib/bioroebe/sequence/protein.rb
720
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  - lib/bioroebe/sequence/reverse_complement.rb
721
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  - 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
743
  - lib/bioroebe/shell/colours/colours.rb
726
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  - lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml
727
745
  - lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml
728
746
  - lib/bioroebe/shell/configuration/upcase_nucleotides.yml
729
747
  - 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
748
  - lib/bioroebe/shell/help/class.rb
737
749
  - 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
750
  - lib/bioroebe/shell/menu.rb
742
751
  - lib/bioroebe/shell/misc.rb
743
- - lib/bioroebe/shell/prompt.rb
744
- - lib/bioroebe/shell/random.rb
745
752
  - 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
753
  - 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
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  - lib/bioroebe/siRNA/README.md
758
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  - lib/bioroebe/siRNA/siRNA.rb
759
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  - lib/bioroebe/string_matching/README.md
@@ -1025,7 +1022,7 @@ post_install_message: |2+
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  For more documentation, have a look at:
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- https://www.rubydoc.info/gems/bioroebe/0.10.80
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+ https://www.rubydoc.info/gems/bioroebe/0.11.24
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  rdoc_options: []
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  require_paths:
@@ -1039,13 +1036,13 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 3.3.16
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+ version: 3.3.18
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  requirements: []
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- rubygems_version: 3.3.16
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+ rubygems_version: 3.3.18
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  signing_key:
1046
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  specification_version: 4
1047
- summary: 'Welcome to the bioroebe-0.10.x release series! It is recommended to use
1048
- ruby 3.x for this series, as it is the most tested version of ruby in regards to
1044
+ summary: 'Welcome to the bioroebe-0.11.x release series! It is recommended to use
1045
+ ruby 3.x for this series, as it is the most tested version of ruby in regards to
1049
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  this project. The bioroebe-project is a software suite focusing on bio-related
1050
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  life sciences in general - in particular molecular biology, molecular genetics,
1051
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  bioinformatics, biotechnology, system biology, synthetic biology and related topics