bioroebe 0.10.80 → 0.11.32

Sign up to get free protection for your applications and to get access to all the features.

Potentially problematic release.

This version of bioroebe might be problematic. Click here for more details.

Files changed (210) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3209 -2618
  3. data/bin/bioroebe +7 -1
  4. data/bioroebe.gemspec +3 -3
  5. data/doc/README.gen +3208 -2617
  6. data/doc/quality_control/commandline_applications.md +3 -3
  7. data/doc/todo/bioroebe_todo.md +2040 -2615
  8. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  9. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  10. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  11. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  12. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  13. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  14. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
  15. data/lib/bioroebe/base/commandline_application/misc.rb +26 -9
  16. data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
  17. data/lib/bioroebe/base/commandline_application/reset.rb +3 -2
  18. data/lib/bioroebe/base/misc.rb +35 -0
  19. data/lib/bioroebe/base/prototype/misc.rb +11 -1
  20. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
  21. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
  22. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  23. data/lib/bioroebe/codons/show_codon_usage.rb +2 -1
  24. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  25. data/lib/bioroebe/constants/database_constants.rb +1 -1
  26. data/lib/bioroebe/constants/files_and_directories.rb +31 -4
  27. data/lib/bioroebe/constants/misc.rb +20 -0
  28. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  29. data/lib/bioroebe/crystal/README.md +2 -0
  30. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  31. data/lib/bioroebe/data/README.md +11 -8
  32. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  33. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  34. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
  35. data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
  36. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
  37. data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
  38. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
  39. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
  40. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  41. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
  42. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
  43. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
  44. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
  45. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1460 -7
  46. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
  47. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  48. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
  49. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
  50. data/lib/bioroebe/genome/README.md +4 -0
  51. data/lib/bioroebe/genome/genome.rb +67 -0
  52. data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
  53. data/lib/bioroebe/gui/gtk +1 -0
  54. data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
  55. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
  56. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +99 -21
  57. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
  58. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
  59. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  60. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  61. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
  62. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  63. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
  64. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
  65. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
  66. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
  67. data/lib/bioroebe/java/README.md +4 -0
  68. data/lib/bioroebe/java/bioroebe/Sequence.java +25 -1
  69. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.class +0 -0
  70. data/lib/bioroebe/java/bioroebe/{Base.java → src/main/java/bioroebe/Base.java} +15 -2
  71. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/main/java/bioroebe/BisulfiteTreatment.class} +0 -0
  72. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/main/java/bioroebe/BisulfiteTreatment.java} +0 -0
  73. data/lib/bioroebe/java/bioroebe/{Codons.class → src/main/java/bioroebe/Codons.class} +0 -0
  74. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java +34 -0
  75. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.class +0 -0
  76. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java +95 -0
  77. data/lib/bioroebe/java/bioroebe/{Esystem.class → src/main/java/bioroebe/Esystem.class} +0 -0
  78. data/lib/bioroebe/java/bioroebe/{Esystem.java → src/main/java/bioroebe/Esystem.java} +0 -0
  79. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/main/java/bioroebe/GenerateRandomDnaSequence.class} +0 -0
  80. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/main/java/bioroebe/GenerateRandomDnaSequence.java} +8 -2
  81. data/lib/bioroebe/java/bioroebe/{IsPalindrome.class → src/main/java/bioroebe/IsPalindrome.class} +0 -0
  82. data/lib/bioroebe/java/bioroebe/{IsPalindrome.java → src/main/java/bioroebe/IsPalindrome.java} +5 -1
  83. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.class +0 -0
  84. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java +56 -0
  85. data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/main/java/bioroebe/RemoveFile.class} +0 -0
  86. data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/main/java/bioroebe/RemoveFile.java} +10 -4
  87. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/main/java/bioroebe/RemoveNumbers.class} +0 -0
  88. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/main/java/bioroebe/RemoveNumbers.java} +1 -0
  89. data/lib/bioroebe/java/bioroebe/{ToCamelcase.class → src/main/java/bioroebe/ToCamelcase.class} +0 -0
  90. data/lib/bioroebe/java/bioroebe/{ToCamelcase.java → src/main/java/bioroebe/ToCamelcase.java} +3 -3
  91. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.class +0 -0
  92. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java +42 -0
  93. data/lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.class +0 -0
  94. data/lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.java +73 -0
  95. data/lib/bioroebe/misc/ruler.rb +1 -0
  96. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
  97. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
  98. data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
  99. data/lib/bioroebe/parsers/gff.rb +1 -9
  100. data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
  101. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
  102. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
  103. data/lib/bioroebe/pdb/parse_pdb_file.rb +1 -9
  104. data/lib/bioroebe/project/project.rb +1 -1
  105. data/lib/bioroebe/python/README.md +1 -0
  106. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  107. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  108. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  109. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  110. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  111. data/lib/bioroebe/python/mymodule.py +8 -0
  112. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  113. data/lib/bioroebe/python/shell/shell.py +19 -0
  114. data/lib/bioroebe/python/to_rna.py +14 -0
  115. data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
  116. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  117. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  118. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  119. data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
  120. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
  121. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  122. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
  123. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  124. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  125. data/lib/bioroebe/sequence/protein.rb +105 -3
  126. data/lib/bioroebe/sequence/sequence.rb +61 -2
  127. data/lib/bioroebe/shell/menu.rb +3819 -3713
  128. data/lib/bioroebe/shell/misc.rb +51 -4311
  129. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  130. data/lib/bioroebe/shell/shell.rb +11250 -28
  131. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  132. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  133. data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
  134. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  135. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  136. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  137. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  138. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  139. data/lib/bioroebe/taxonomy/info/info.rb +18 -11
  140. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  141. data/lib/bioroebe/taxonomy/interactive.rb +140 -104
  142. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  143. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  144. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  145. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  146. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  147. data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
  148. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  149. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
  150. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
  151. data/lib/bioroebe/toplevel_methods/misc.rb +118 -11
  152. data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
  153. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  154. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  155. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  156. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  157. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  158. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  159. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  160. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  161. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  162. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  163. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  164. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  165. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  166. data/lib/bioroebe/version/version.rb +2 -2
  167. data/lib/bioroebe/www/embeddable_interface.rb +101 -52
  168. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  169. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  170. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  171. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  172. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
  173. metadata +69 -64
  174. data/doc/setup.rb +0 -1655
  175. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
  176. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
  177. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
  178. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
  179. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
  180. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
  181. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  182. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  183. data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
  184. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  185. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
  186. data/lib/bioroebe/java/bioroebe.jar +0 -0
  187. data/lib/bioroebe/shell/add.rb +0 -108
  188. data/lib/bioroebe/shell/assign.rb +0 -360
  189. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  190. data/lib/bioroebe/shell/constants.rb +0 -166
  191. data/lib/bioroebe/shell/download.rb +0 -335
  192. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  193. data/lib/bioroebe/shell/enzymes.rb +0 -310
  194. data/lib/bioroebe/shell/fasta.rb +0 -345
  195. data/lib/bioroebe/shell/gtk.rb +0 -76
  196. data/lib/bioroebe/shell/history.rb +0 -132
  197. data/lib/bioroebe/shell/initialize.rb +0 -217
  198. data/lib/bioroebe/shell/loop.rb +0 -74
  199. data/lib/bioroebe/shell/prompt.rb +0 -107
  200. data/lib/bioroebe/shell/random.rb +0 -289
  201. data/lib/bioroebe/shell/reset.rb +0 -335
  202. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  203. data/lib/bioroebe/shell/search.rb +0 -337
  204. data/lib/bioroebe/shell/sequences.rb +0 -200
  205. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  206. data/lib/bioroebe/shell/startup.rb +0 -127
  207. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  208. data/lib/bioroebe/shell/tk.rb +0 -23
  209. data/lib/bioroebe/shell/user_input.rb +0 -88
  210. data/lib/bioroebe/shell/xorg.rb +0 -45
data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb DELETED
@@ -1,50 +0,0 @@
1
- #!/usr/bin/ruby -w
2
- # Encoding: UTF-8
3
- # frozen_string_literal: true
4
- # =========================================================================== #
5
- # require 'bioroebe/fasta_and_fastq/parse_fasta/constants.rb'
6
- # =========================================================================== #
7
- require 'bioroebe/base/commandline_application/commandline_application.rb'
8
-
9
- module Bioroebe
10
-
11
- class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
12
-
13
- # ========================================================================= #
14
- # === NAMESPACE
15
- # ========================================================================= #
16
- NAMESPACE = inspect
17
-
18
- # ========================================================================= #
19
- # === REGEX_NON_NUCLEOTIDES
20
- #
21
- # All non-nucleotides will be handled here via this regex.
22
- #
23
- # N is excluded because it may stand for "any" nucleotide too, at
24
- # the least for a purine.
25
- # ========================================================================= #
26
- REGEX_NON_NUCLEOTIDES =
27
- /BDEFHIJKLMOPQRSVWXYZ/
28
-
29
- # ========================================================================= #
30
- # === DEFAULT_FASTA
31
- #
32
- # This String can be used to quickly test code depending on FASTA
33
- # entries.
34
- # ========================================================================= #
35
- DEFAULT_FASTA = '>Rosalind_6404
36
- CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
37
- TCCCACTAATAATTCTGAGG
38
- >Rosalind_5959
39
- CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
40
- ATATCCATTTGTCAGCAGACACGC
41
- >Rosalind_0808
42
- CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
43
- TGGGAACCTGCGGGCAGTAGGTGGAAT'
44
-
45
- # ========================================================================= #
46
- # === DEFAULT_ROUND_TO
47
- # ========================================================================= #
48
- DEFAULT_ROUND_TO = 2
49
-
50
- end; end
data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb DELETED
@@ -1,86 +0,0 @@
1
- #!/usr/bin/ruby -w
2
- # Encoding: UTF-8
3
- # frozen_string_literal: true
4
- # =========================================================================== #
5
- # require 'bioroebe/fasta_and_fastq/parse_fasta/initialize.rb'
6
- # =========================================================================== #
7
- module Bioroebe
8
-
9
- class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
10
-
11
- # ========================================================================= #
12
- # === initialize
13
- # ========================================================================= #
14
- def initialize(
15
- i = DEFAULT_FASTA,
16
- run_already = true,
17
- &block
18
- )
19
- reset
20
- # ======================================================================= #
21
- # === Handle blocks next
22
- # ======================================================================= #
23
- if block_given?
24
- yielded = yield
25
- # ===================================================================== #
26
- # First handle Symbols.
27
- # ===================================================================== #
28
- case yielded
29
- # ===================================================================== #
30
- # === :be_verbose
31
- # ===================================================================== #
32
- when :be_verbose,
33
- :verbose
34
- set_be_verbose_and_report_the_sequence
35
- # ===================================================================== #
36
- # === :be_quiet
37
- # ===================================================================== #
38
- when :be_quiet,
39
- :be_silent
40
- be_quiet
41
- # ===================================================================== #
42
- # === :sizeseq
43
- # ===================================================================== #
44
- when :sizeseq
45
- @sort_by_size = true
46
- end
47
- # ===================================================================== #
48
- # === Handle Hashes next
49
- # ===================================================================== #
50
- if yielded.is_a? Hash
51
- # =================================================================== #
52
- # === :be_verbose
53
- # =================================================================== #
54
- if yielded.has_key? :be_verbose
55
- set_be_verbose(yielded.delete(:be_verbose))
56
- @internal_hash[:report_the_sequence] = true
57
- end
58
- # =================================================================== #
59
- # === :use_colours
60
- # =================================================================== #
61
- if yielded.has_key? :use_colours
62
- set_use_colours(
63
- yielded.delete(:use_colours)
64
- )
65
- end
66
- # =================================================================== #
67
- # === :sizeseq
68
- # =================================================================== #
69
- if yielded.has_key? :sizeseq
70
- @sort_by_size = true
71
- end
72
- end
73
- end
74
- set_commandline_arguments(i)
75
- case run_already
76
- # ======================================================================= #
77
- # === :dont_run_yet
78
- # ======================================================================= #
79
- when :dont_run_yet,
80
- :do_not_run_yet
81
- run_already = false
82
- end
83
- run if run_already
84
- end
85
-
86
- end; end
data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb DELETED
@@ -1,117 +0,0 @@
1
- #!/usr/bin/ruby -w
2
- # Encoding: UTF-8
3
- # frozen_string_literal: true
4
- # =========================================================================== #
5
- # require 'bioroebe/fasta_and_fastq/parse_fasta/menu.rb'
6
- # =========================================================================== #
7
- module Bioroebe
8
-
9
- class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
10
-
11
- # ========================================================================= #
12
- # === menu (menu tag)
13
- # ========================================================================= #
14
- def menu(
15
- i = return_commandline_arguments_that_are_not_files
16
- )
17
- if i.is_a? Array
18
- i.each {|entry| menu(entry) }
19
- else
20
- case i # case tag
21
- # ===================================================================== #
22
- # === --to-protein
23
- #
24
- # Invocation example:
25
- #
26
- # pfasta *.fasta --toprotein
27
- #
28
- # ===================================================================== #
29
- when /^-?-?to(-|_)?protein/i
30
- @internal_hash[:show_the_translated_protein_sequence] = true
31
- # ===================================================================== #
32
- # === --one-line
33
- #
34
- # Invocation example:
35
- #
36
- # pfasta rpoS_NC_000913.3.fasta --one-line
37
- #
38
- # ===================================================================== #
39
- when /^-?-?one(-|_)?liner?/i
40
- @internal_hash[:condense_the_sequence_onto_a_single_line] = true
41
- # ===================================================================== #
42
- # === --limit=1000
43
- #
44
- # Invocation example:
45
- #
46
- # pfasta --limit=1000
47
- #
48
- # ===================================================================== #
49
- when /^-?-?limit=(\d+)$/i
50
- @internal_hash[:limit_the_display_to_n_nucleotides] = $1.to_s.dup.to_i
51
- # ===================================================================== #
52
- # === --overwrite
53
- # ===================================================================== #
54
- when /^-?-?overwrite/i
55
- @internal_hash[:overwrite_the_original_file] = true
56
- # ===================================================================== #
57
- # === --help
58
- #
59
- # Usage example:
60
- #
61
- # parse_fasta --help
62
- #
63
- # ===================================================================== #
64
- when /^-?-?help/i
65
- show_help
66
- exit
67
- # ===================================================================== #
68
- # === --save-file
69
- # ===================================================================== #
70
- when /^-?-?save(-|_)?file/i
71
- @internal_hash[:save_the_file] = true
72
- # ===================================================================== #
73
- # === --also-show-the-sequence
74
- #
75
- # To invoke this method try:
76
- #
77
- # parsefasta /Depot/Bioroebe/NP_013521.3_289_aa.fasta --show
78
- #
79
- # ===================================================================== #
80
- when /^-?-?also(-|_)?show(-|_)?the(-|_)?sequence$/i,
81
- /^-?-?report$/i,
82
- /^-?-?show$/i
83
- @internal_hash[:report_the_sequence] = true
84
- # ===================================================================== #
85
- # === --header
86
- # ===================================================================== #
87
- when /^-?-?header/i
88
- do_show_the_header
89
- # ===================================================================== #
90
- # === --short
91
- #
92
- # This entry point can be used to show 300 nucleotides and not
93
- # more, by simply using the --short commandline flag.
94
- # ===================================================================== #
95
- when /^-?-?short/i
96
- @internal_hash[:limit_the_display_to_n_nucleotides] = 300
97
- # ===================================================================== #
98
- # === --size
99
- #
100
- # This will simply tell us how many nucleotides the given sequence
101
- # has, then exit.
102
- #
103
- # To invoke this method try:
104
- #
105
- # parsefasta /Depot/Bioroebe/NP_013521.3_289_aa.fasta --size
106
- #
107
- # ===================================================================== #
108
- when /^-?-?size$/i
109
- set_be_quiet
110
- do_process_the_commandline_arguments_that_are_files
111
- erev size? # Report the size here.
112
- exit
113
- end
114
- end
115
- end
116
-
117
- end; end