bioroebe 0.10.80 → 0.11.25

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Files changed (134) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3117 -2645
  3. data/bioroebe.gemspec +3 -3
  4. data/doc/README.gen +3116 -2644
  5. data/doc/todo/bioroebe_todo.md +418 -387
  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 +24 -4
  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/gtk +1 -0
  34. data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
  35. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
  36. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
  37. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
  38. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  39. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  40. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  41. data/lib/bioroebe/misc/ruler.rb +1 -0
  42. data/lib/bioroebe/parsers/genbank_parser.rb +353 -24
  43. data/lib/bioroebe/parsers/gff.rb +1 -9
  44. data/lib/bioroebe/pdb/parse_pdb_file.rb +1 -9
  45. data/lib/bioroebe/project/project.rb +1 -1
  46. data/lib/bioroebe/python/README.md +1 -0
  47. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  48. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  49. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  50. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  51. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  52. data/lib/bioroebe/python/mymodule.py +8 -0
  53. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  54. data/lib/bioroebe/python/shell/shell.py +19 -0
  55. data/lib/bioroebe/python/to_rna.py +14 -0
  56. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  57. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  58. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  59. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +34 -0
  60. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  61. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +11 -0
  62. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  63. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  64. data/lib/bioroebe/sequence/protein.rb +105 -3
  65. data/lib/bioroebe/sequence/sequence.rb +61 -2
  66. data/lib/bioroebe/shell/menu.rb +3752 -3667
  67. data/lib/bioroebe/shell/misc.rb +51 -4311
  68. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  69. data/lib/bioroebe/shell/shell.rb +11199 -28
  70. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  71. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  72. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  73. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  74. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  75. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  76. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  77. data/lib/bioroebe/taxonomy/info/info.rb +17 -2
  78. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  79. data/lib/bioroebe/taxonomy/interactive.rb +139 -95
  80. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  81. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  82. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  83. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  84. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  85. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  86. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +101 -63
  87. data/lib/bioroebe/toplevel_methods/misc.rb +17 -16
  88. data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
  89. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  90. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  91. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  92. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  93. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  94. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  95. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  96. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  97. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  98. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  99. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  100. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  101. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  102. data/lib/bioroebe/version/version.rb +2 -2
  103. data/lib/bioroebe/www/embeddable_interface.rb +101 -52
  104. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  105. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  106. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  107. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  108. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
  109. metadata +33 -35
  110. data/doc/setup.rb +0 -1655
  111. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  112. data/lib/bioroebe/shell/add.rb +0 -108
  113. data/lib/bioroebe/shell/assign.rb +0 -360
  114. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  115. data/lib/bioroebe/shell/constants.rb +0 -166
  116. data/lib/bioroebe/shell/download.rb +0 -335
  117. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  118. data/lib/bioroebe/shell/enzymes.rb +0 -310
  119. data/lib/bioroebe/shell/fasta.rb +0 -345
  120. data/lib/bioroebe/shell/gtk.rb +0 -76
  121. data/lib/bioroebe/shell/history.rb +0 -132
  122. data/lib/bioroebe/shell/initialize.rb +0 -217
  123. data/lib/bioroebe/shell/loop.rb +0 -74
  124. data/lib/bioroebe/shell/prompt.rb +0 -107
  125. data/lib/bioroebe/shell/random.rb +0 -289
  126. data/lib/bioroebe/shell/reset.rb +0 -335
  127. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  128. data/lib/bioroebe/shell/search.rb +0 -337
  129. data/lib/bioroebe/shell/sequences.rb +0 -200
  130. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  131. data/lib/bioroebe/shell/startup.rb +0 -127
  132. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  133. data/lib/bioroebe/shell/user_input.rb +0 -88
  134. data/lib/bioroebe/shell/xorg.rb +0 -45
data/lib/bioroebe/data/electron_microscopy/pos_example.pos ADDED
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+ # XMIPP_STAR_1 *
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+ #
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+ data_mic_1_36kx_4
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+ loop_
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+ 2741 2405 2.000000
357
+ 2742 2437 2.000000
358
+ 2479 2091 2.000000
359
+ 2458 2107 2.000000
360
+ 3164 2271 2.000000
361
+ 3138 2278 2.000000
362
+ 3085 2290 2.000000
363
+ 3057 2315 2.000000
364
+ 3030 2298 2.000000
365
+ 2973 2318 2.000000
366
+ 2945 2378 2.000000
367
+ 3037 2409 2.000000
368
+ 2928 1896 2.000000
369
+ 2908 1888 2.000000
370
+ 2986 1901 2.000000
371
+ 3006 1875 2.000000
372
+ 3036 1890 2.000000
373
+ 2924 1770 2.000000
374
+ 2921 1736 2.000000
375
+ 2865 1732 2.000000
376
+ 3010 1654 2.000000
377
+ 3009 1630 2.000000
378
+ 3000 1769 2.000000
379
+ 3020 1530 2.000000
380
+ 3079 1510 2.000000
381
+ 3119 1528 2.000000
382
+ 2247 1782 2.000000
383
+ 2486 1305 2.000000
384
+ 2608 1274 2.000000
385
+ 3063 1436 2.000000
386
+ 2964 1424 2.000000
387
+ 1961 883 2.000000
388
+ 1966 862 2.000000
389
+ 2410 785 2.000000
390
+ 3082 1221 2.000000
391
+ 3170 1103 2.000000
392
+ 2037 1232 2.000000
393
+ 2349 1462 2.000000
394
+ 581 213 2.000000
395
+ 593 764 2.000000
396
+ 1393 237 2.000000
data/lib/bioroebe/data/electron_microscopy/test_particles.star ADDED
@@ -0,0 +1,36 @@
1
+
2
+ data_images
3
+
4
+ loop_
5
+ _rlnImageName #1
6
+ _rlnCoordinateX #2
7
+ _rlnCoordinateY #3
8
+ _rlnMicrographName #4
9
+ 000001@Particles/Micrographs/1_36kx_6_particles.mrcs 283.000000 285.000000 Micrographs/1_36kx_6.mrc
10
+ 000002@Particles/Micrographs/1_36kx_6_particles.mrcs 187.000000 232.000000 Micrographs/1_36kx_6.mrc
11
+ 000003@Particles/Micrographs/1_36kx_6_particles.mrcs 661.000000 377.000000 Micrographs/1_36kx_6.mrc
12
+ 000004@Particles/Micrographs/1_36kx_6_particles.mrcs 702.000000 386.000000 Micrographs/1_36kx_6.mrc
13
+ 000005@Particles/Micrographs/1_36kx_6_particles.mrcs 684.000000 407.000000 Micrographs/1_36kx_6.mrc
14
+ 000006@Particles/Micrographs/1_36kx_6_particles.mrcs 684.000000 591.000000 Micrographs/1_36kx_6.mrc
15
+ 000007@Particles/Micrographs/1_36kx_6_particles.mrcs 810.000000 297.000000 Micrographs/1_36kx_6.mrc
16
+ 000008@Particles/Micrographs/1_36kx_6_particles.mrcs 786.000000 244.000000 Micrographs/1_36kx_6.mrc
17
+ 000009@Particles/Micrographs/1_36kx_6_particles.mrcs 826.000000 247.000000 Micrographs/1_36kx_6.mrc
18
+ 000010@Particles/Micrographs/1_36kx_6_particles.mrcs 847.000000 240.000000 Micrographs/1_36kx_6.mrc
19
+ 000011@Particles/Micrographs/1_36kx_6_particles.mrcs 927.000000 376.000000 Micrographs/1_36kx_6.mrc
20
+ 000012@Particles/Micrographs/1_36kx_6_particles.mrcs 930.000000 380.000000 Micrographs/1_36kx_6.mrc
21
+ 000013@Particles/Micrographs/1_36kx_6_particles.mrcs 967.000000 412.000000 Micrographs/1_36kx_6.mrc
22
+ 000014@Particles/Micrographs/1_36kx_6_particles.mrcs 948.000000 417.000000 Micrographs/1_36kx_6.mrc
23
+ 000015@Particles/Micrographs/1_36kx_6_particles.mrcs 802.000000 552.000000 Micrographs/1_36kx_6.mrc
24
+ 000016@Particles/Micrographs/1_36kx_6_particles.mrcs 778.000000 547.000000 Micrographs/1_36kx_6.mrc
25
+ 000017@Particles/Micrographs/1_36kx_6_particles.mrcs 652.000000 549.000000 Micrographs/1_36kx_6.mrc
26
+ 000018@Particles/Micrographs/1_36kx_6_particles.mrcs 464.000000 533.000000 Micrographs/1_36kx_6.mrc
27
+ 000019@Particles/Micrographs/1_36kx_6_particles.mrcs 278.000000 653.000000 Micrographs/1_36kx_6.mrc
28
+ 000020@Particles/Micrographs/1_36kx_6_particles.mrcs 1052.000000 653.000000 Micrographs/1_36kx_6.mrc
29
+ 000021@Particles/Micrographs/1_36kx_6_particles.mrcs 1143.000000 671.000000 Micrographs/1_36kx_6.mrc
30
+ 000022@Particles/Micrographs/1_36kx_6_particles.mrcs 1095.000000 119.000000 Micrographs/1_36kx_6.mrc
31
+ 000023@Particles/Micrographs/1_36kx_6_particles.mrcs 1131.000000 102.000000 Micrographs/1_36kx_6.mrc
32
+ 000024@Particles/Micrographs/1_36kx_6_particles.mrcs 1148.000000 122.000000 Micrographs/1_36kx_6.mrc
33
+ 000025@Particles/Micrographs/1_36kx_6_particles.mrcs 434.000000 103.000000 Micrographs/1_36kx_6.mrc
34
+ 000026@Particles/Micrographs/1_36kx_6_particles.mrcs 324.000000 72.000000 Micrographs/1_36kx_6.mrc
35
+ 000027@Particles/Micrographs/1_36kx_6_particles.mrcs 82.000000 83.000000 Micrographs/1_36kx_6.mrc
36
+ 000028@Particles/Micrographs/1_36kx_6_particles.mrcs 196.000000 495.000000 Micrographs/1_36kx_6.mrc
data/lib/bioroebe/{shell/tk.rb → electron_microscopy/electron_microscopy_module.rb} RENAMED
@@ -2,22 +2,27 @@
2
2
  # Encoding: UTF-8
3
3
  # frozen_string_literal: true
4
4
  # =========================================================================== #
5
- # require 'bioroebe/shell/tk.rb'
5
+ # require 'bioroebe/electron_microscopy/electron_microscopy_module.rb'
6
+ # include Bioroebe::ElectronMicroscopy
6
7
  # =========================================================================== #
7
- require 'bioroebe/base/commandline_application/commandline_application.rb'
8
-
9
8
  module Bioroebe
10
9
 
11
- class Shell < ::Bioroebe::CommandlineApplication
10
+ module ElectronMicroscopy
12
11
 
13
12
  # ========================================================================= #
14
- # === start_three_to_one
13
+ # === DEFAULT_XMIPP_HEADER
15
14
  #
16
- # Mostly an ad-hoc way to load up a specific ruby-tk widget.
15
+ # The header for xmipp.
17
16
  # ========================================================================= #
18
- def tk_start_three_to_one
19
- require 'bioroebe/gui/tk/three_to_one/three_to_one.rb'
20
- Bioroebe::GUI::Tk::ThreeToOne.new(ARGV)
21
- end
17
+ DEFAULT_XMIPP_HEADER = '# XMIPP_STAR_1 *
18
+ #
19
+ data_noname
20
+ loop_
21
+ _image
22
+ _micrograph
23
+ _xcoor
24
+ _ycoor
25
+
26
+ '
22
27
 
23
28
  end; end
data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb CHANGED
@@ -22,10 +22,8 @@ module ElectronMicroscopy
22
22
 
23
23
  class SimpleStarFileGenerator < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::SimpleStarFileGenerator
24
24
 
25
- # ========================================================================= #
26
- # === NAMESPACE
27
- # ========================================================================= #
28
- NAMESPACE = inspect
25
+ require 'bioroebe/electron_microscopy/electron_microscopy_module.rb'
26
+ include Bioroebe::ElectronMicroscopy
29
27
 
30
28
  # ========================================================================= #
31
29
  # === SAVE_HERE
@@ -62,14 +60,11 @@ _rlnMicrographName #1'+N
62
60
  end
63
61
 
64
62
  # ========================================================================= #
65
- # === reset
63
+ # === reset (reset tag)
66
64
  # ========================================================================= #
67
65
  def reset
68
66
  super()
69
- # ======================================================================= #
70
- # === @namespace
71
- # ======================================================================= #
72
- @namespace = NAMESPACE
67
+ infer_the_namespace
73
68
  # ======================================================================= #
74
69
  # === @save_here
75
70
  # ======================================================================= #
data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb CHANGED
@@ -86,17 +86,6 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
86
86
  @input
87
87
  end
88
88
 
89
- # ========================================================================= #
90
- # === report_this_header_from_that_file
91
- # ========================================================================= #
92
- def report_this_header_from_that_file(header, file)
93
- if @be_verbose
94
- erev "The file at #{sfile(file)}#{rev} has the following FASTA header:"
95
- e
96
- end
97
- e " #{simp(header)}"
98
- end
99
-
100
89
  # ========================================================================= #
101
90
  # === input_without_extension
102
91
  # ========================================================================= #
@@ -116,13 +105,39 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
116
105
  }
117
106
  end
118
107
 
108
+ # ========================================================================= #
109
+ # === report_this_header_from_that_file
110
+ # ========================================================================= #
111
+ def report_this_header_from_that_file(header, file)
112
+ if @be_verbose
113
+ erev "The file at #{sfile(file)}#{rev} has the following FASTA header:"
114
+ e
115
+ end
116
+ e " #{simp(header)}"
117
+ if header.include? '|'
118
+ splitted = header.split('|')
119
+ if splitted.size > 2
120
+ assumed_name_of_the_organism = splitted[2].strip
121
+ if assumed_name_of_the_organism.include? 'OS='
122
+ assumed_name_of_the_organism = assumed_name_of_the_organism.scan(/ OS=(.+)/).flatten
123
+ assumed_name_of_the_organism = assumed_name_of_the_organism.first
124
+ if assumed_name_of_the_organism.include? ' ('
125
+ assumed_name_of_the_organism = assumed_name_of_the_organism.split(' (').first
126
+ end
127
+ end
128
+ erev 'The organism may be: '+
129
+ steelblue(assumed_name_of_the_organism)+rev
130
+ end
131
+ end
132
+ end
133
+
119
134
  # ========================================================================= #
120
135
  # === run (run tag)
121
136
  # ========================================================================= #
122
137
  def run
123
138
  files = Dir[input?]
124
139
  if files.empty?
125
- opnn; e 'No files could be found for '+input?+'.'
140
+ opnn; e "No files could be found for #{input?}."
126
141
  else
127
142
  report_these_files(files)
128
143
  end
data/lib/bioroebe/genome/README.md ADDED
@@ -0,0 +1,4 @@
1
+ This directory was created on the 12.07.2022.
2
+
3
+ The idea is that we can make use of class Bioroebe::Genome
4
+ to represent a genome.
data/lib/bioroebe/genome/genome.rb ADDED
@@ -0,0 +1,67 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
4
+ # =========================================================================== #
5
+ # === Bioroebe::Genome
6
+ #
7
+ # This class should be able to represent a genome.
8
+ #
9
+ # Usage example:
10
+ #
11
+ # Bioroebe::Genome.new(ARGV)
12
+ #
13
+ # =========================================================================== #
14
+ # require 'bioroebe/genome/genome.rb'
15
+ # =========================================================================== #
16
+ module Bioroebe
17
+
18
+ class Genome # < Base # === Bioroebe::Genome
19
+
20
+ # ========================================================================= #
21
+ # === NAMESPACE
22
+ # ========================================================================= #
23
+ NAMESPACE = inspect
24
+
25
+ # ========================================================================= #
26
+ # === initialize
27
+ # ========================================================================= #
28
+ def initialize(
29
+ commandline_arguments = nil,
30
+ run_already = true
31
+ )
32
+ reset
33
+ set_commandline_arguments(
34
+ commandline_arguments
35
+ )
36
+ run if run_already
37
+ end
38
+
39
+ # ========================================================================= #
40
+ # === reset (reset tag)
41
+ # ========================================================================= #
42
+ def reset
43
+ super()
44
+ # ======================================================================= #
45
+ # === @namespace
46
+ # ======================================================================= #
47
+ @namespace = NAMESPACE
48
+ end
49
+
50
+ # ========================================================================= #
51
+ # === run (run tag)
52
+ # ========================================================================= #
53
+ def run
54
+ end
55
+
56
+ # ========================================================================= #
57
+ # === Bioroebe::Genome[]
58
+ # ========================================================================= #
59
+ def self.[](i = '')
60
+ new(i)
61
+ end
62
+
63
+ end; end
64
+
65
+ if __FILE__ == $PROGRAM_NAME
66
+ Bioroebe::Genome.new(ARGV)
67
+ end # genome
data/lib/bioroebe/gui/gtk ADDED
@@ -0,0 +1 @@
1
+ gtk3