bioroebe 0.10.80 → 0.11.32

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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/data/electron_microscopy/pos_example.pos ADDED
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+ # XMIPP_STAR_1 *
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+ #
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+ loop_
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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/electron_microscopy/coordinate_analyzer.rb CHANGED
@@ -19,11 +19,6 @@ module ElectronMicroscopy
19
19
 
20
20
  class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::CoordinateAnalyzer
21
21
 
22
- # =========================================================================== #
23
- # === NAMESPACE
24
- # =========================================================================== #
25
- NAMESPACE = inspect
26
-
27
22
  # =========================================================================== #
28
23
  # === STORE_HERE
29
24
  # =========================================================================== #
@@ -44,10 +39,7 @@ class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::El
44
39
  # =========================================================================== #
45
40
  def reset
46
41
  super()
47
- # ========================================================================= #
48
- # === @namespace
49
- # ========================================================================= #
50
- @namespace = NAMESPACE
42
+ infer_the_namespace
51
43
  # ========================================================================= #
52
44
  # === @dataset
53
45
  # ========================================================================= #
@@ -71,7 +63,7 @@ class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::El
71
63
  # Which internal base directory to use.
72
64
  # =========================================================================== #
73
65
  def base?
74
- "#{ROEBE_HOME_DIR}Image*"
66
+ "#{log_dir?}image*"
75
67
  end
76
68
 
77
69
  # =========================================================================== #
@@ -94,10 +86,10 @@ class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::El
94
86
  # =========================================================================== #
95
87
  def analyze_dataset
96
88
  if @dataset.empty?
97
- opnn; e 'Can not analyze anything as the dataset (from '+
98
- simp(base?)+') is empty.'
89
+ erev 'Can not analyze anything as the dataset (from '+
90
+ simp(base?)+rev+') is empty.'
99
91
  else
100
- opnn; e 'Analyzing the dataset.'
92
+ erev 'Analyzing the dataset.'
101
93
  @dataset.sort.each_with_index {|entry, index|
102
94
  index += 1
103
95
  index = '%02d' % index
@@ -105,7 +97,7 @@ class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::El
105
97
  data = data.select {|inner_entry| inner_entry.include? ' ' }
106
98
  n_lines = data.size
107
99
  entry = '%-41s' % entry
108
- opnn; e ' '+sfile(entry)+' has '+simp(n_lines.to_s)+' particles.'
100
+ erev ' '+sfile(entry)+rev+' has '+simp(n_lines.to_s)+rev+' particles.'
109
101
  # Next, we store this directly into the file.
110
102
  append_what_into('Image '+index+': '+n_lines.to_s+N, store_where?)
111
103
  @n_total_particles += n_lines
@@ -132,16 +124,21 @@ class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::El
132
124
  # It will generate the file total_amount_of_particles.
133
125
  # =========================================================================== #
134
126
  def generate_a_report
135
- opnn; e "Now generating a report into `#{sfile(store_where?)}`."
136
- append_what_into(N+N+'Total: '+@n_total_particles.to_s+N,
137
- store_where?)
127
+ erev "Now generating a report into `#{sfile(store_where?)}#{rev}`."
128
+ append_what_into(
129
+ N+N+'Total: '+@n_total_particles.to_s+N,
130
+ store_where?
131
+ )
138
132
  end
139
133
 
140
134
  # =========================================================================== #
141
135
  # === startup_message
142
136
  # =========================================================================== #
143
137
  def startup_message
144
- opnn; e 'We attempt to analyze the coordinates next.'
138
+ opnn { :no_trailing }
139
+ e
140
+ e
141
+ erev 'Attempting to analyze the coordinates next.'
145
142
  end
146
143
 
147
144
  # =========================================================================== #
data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} RENAMED
@@ -2,19 +2,27 @@
2
2
  # Encoding: UTF-8
3
3
  # frozen_string_literal: true
4
4
  # =========================================================================== #
5
- # require 'bioroebe/fasta_and_fastq/parse_fasta/run.rb'
5
+ # require 'bioroebe/electron_microscopy/electron_microscopy_module.rb'
6
+ # include Bioroebe::ElectronMicroscopy
6
7
  # =========================================================================== #
7
8
  module Bioroebe
8
9
 
9
- class ParseFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseFasta
10
+ module ElectronMicroscopy
10
11
 
11
12
  # ========================================================================= #
12
- # === run (run tag)
13
+ # === DEFAULT_XMIPP_HEADER
14
+ #
15
+ # The header for xmipp.
13
16
  # ========================================================================= #
14
- def run
15
- menu
16
- do_process_the_commandline_arguments_that_are_files
17
- do_save_the_file if save_the_file?
18
- end
17
+ DEFAULT_XMIPP_HEADER = '# XMIPP_STAR_1 *
18
+ #
19
+ data_noname
20
+ loop_
21
+ _image
22
+ _micrograph
23
+ _xcoor
24
+ _ycoor
25
+
26
+ '
19
27
 
20
28
  end; end
data/lib/bioroebe/electron_microscopy/fix_pos_file.rb CHANGED
@@ -18,11 +18,6 @@ class FixPosFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMi
18
18
 
19
19
  require 'bioroebe/electron_microscopy/parse_coordinates.rb'
20
20
 
21
- # ========================================================================= #
22
- # === NAMESPACE
23
- # ========================================================================= #
24
- NAMESPACE = inspect
25
-
26
21
  # ========================================================================= #
27
22
  # === initialize
28
23
  # ========================================================================= #
@@ -43,10 +38,7 @@ class FixPosFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMi
43
38
  def reset
44
39
  super()
45
40
  set_fix_this_pos_file
46
- # ======================================================================= #
47
- # === @namespace
48
- # ======================================================================= #
49
- @namespace = NAMESPACE
41
+ infer_the_namespace
50
42
  end
51
43
 
52
44
  # ========================================================================= #
data/lib/bioroebe/electron_microscopy/flipy.rb ADDED
@@ -0,0 +1,83 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
4
+ # ========================================================================= #
5
+ # === Bioroebe::ElectronMicroscopy::FlipY
6
+ #
7
+ # This class will flip the coordinates in the y-axis direction. It will
8
+ # work on .mrc files.
9
+ #
10
+ # Usage example:
11
+ #
12
+ # Bioroebe::ElectronMicroscopy/FlipY.new
13
+ #
14
+ # ========================================================================= #
15
+ # require 'bioroebe/electron_microscopy/flipy.rb'
16
+ # ========================================================================= #
17
+ require 'bioroebe/base/commandline_application/commandline_application.rb'
18
+
19
+ module Bioroebe
20
+
21
+ module ElectronMicroscopy
22
+
23
+ class FlipY < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::FlipY
24
+
25
+ # ========================================================================= #
26
+ # === initialize
27
+ # ========================================================================= #
28
+ def initialize(
29
+ i = nil,
30
+ run_already = true
31
+ )
32
+ reset
33
+ set_commandline_arguments(i)
34
+ run if run_already
35
+ end
36
+
37
+ # ========================================================================= #
38
+ # === reset (reset tag)
39
+ # ========================================================================= #
40
+ def reset
41
+ super()
42
+ infer_the_namespace
43
+ end
44
+
45
+ # ========================================================================= #
46
+ # === menu (menu tag)
47
+ # ========================================================================= #
48
+ def menu(i)
49
+ case i
50
+ # ======================================================================= #
51
+ # === --help
52
+ # ======================================================================= #
53
+ when /^-?-?help$/i
54
+ opnn; e 'Input a .mrc file.'
55
+ exit
56
+ end
57
+ end
58
+
59
+ # ========================================================================= #
60
+ # === run (run tag)
61
+ # ========================================================================= #
62
+ def run
63
+ this_image = first_argument?
64
+ if this_image.is_a? Array
65
+ this_image = this_image.first
66
+ end
67
+ this_image = this_image.to_s
68
+ output_location = (
69
+ File.dirname(this_image)+'/'+File.basename(this_image)
70
+ ).squeeze('/')
71
+ if output_location.include? 'BACKUP/'
72
+ output_location.gsub!(/BACKUP\//, '')
73
+ end
74
+ @cmd = 'xmipp_transform_mirror --flipY -i '+this_image+' -o '+output_location
75
+ menu(this_image)
76
+ esystem @cmd
77
+ end
78
+
79
+ end; end; end
80
+
81
+ if __FILE__ == $PROGRAM_NAME
82
+ Bioroebe::ElectronMicroscopy::FlipY.new(ARGV)
83
+ end # flipy
data/lib/bioroebe/electron_microscopy/parse_coordinates.rb CHANGED
@@ -19,12 +19,7 @@ module Bioroebe
19
19
 
20
20
  module ElectronMicroscopy
21
21
 
22
- class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ParseCoordinates.new
23
-
24
- # ========================================================================= #
25
- # === NAMESPACE
26
- # ========================================================================= #
27
- NAMESPACE = inspect
22
+ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ParseCoordinates
28
23
 
29
24
  # ========================================================================= #
30
25
  # === DEFAULT_FILE
@@ -58,10 +53,7 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
58
53
  # ========================================================================= #
59
54
  def reset
60
55
  super()
61
- # ======================================================================= #
62
- # === @namespace
63
- # ======================================================================= #
64
- @namespace = NAMESPACE
56
+ infer_the_namespace
65
57
  # ======================================================================= #
66
58
  # === @dataset
67
59
  # ======================================================================= #