BioDSL 1.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (197) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +10 -0
  3. data/BioDSL.gemspec +64 -0
  4. data/LICENSE +339 -0
  5. data/README.md +205 -0
  6. data/Rakefile +94 -0
  7. data/examples/fastq_to_fasta.rb +8 -0
  8. data/lib/BioDSL/cary.rb +242 -0
  9. data/lib/BioDSL/command.rb +133 -0
  10. data/lib/BioDSL/commands/add_key.rb +110 -0
  11. data/lib/BioDSL/commands/align_seq_mothur.rb +194 -0
  12. data/lib/BioDSL/commands/analyze_residue_distribution.rb +222 -0
  13. data/lib/BioDSL/commands/assemble_pairs.rb +336 -0
  14. data/lib/BioDSL/commands/assemble_seq_idba.rb +230 -0
  15. data/lib/BioDSL/commands/assemble_seq_ray.rb +345 -0
  16. data/lib/BioDSL/commands/assemble_seq_spades.rb +252 -0
  17. data/lib/BioDSL/commands/classify_seq.rb +217 -0
  18. data/lib/BioDSL/commands/classify_seq_mothur.rb +226 -0
  19. data/lib/BioDSL/commands/clip_primer.rb +318 -0
  20. data/lib/BioDSL/commands/cluster_otus.rb +181 -0
  21. data/lib/BioDSL/commands/collapse_otus.rb +170 -0
  22. data/lib/BioDSL/commands/collect_otus.rb +150 -0
  23. data/lib/BioDSL/commands/complement_seq.rb +117 -0
  24. data/lib/BioDSL/commands/count.rb +135 -0
  25. data/lib/BioDSL/commands/count_values.rb +149 -0
  26. data/lib/BioDSL/commands/degap_seq.rb +253 -0
  27. data/lib/BioDSL/commands/dereplicate_seq.rb +168 -0
  28. data/lib/BioDSL/commands/dump.rb +157 -0
  29. data/lib/BioDSL/commands/filter_rrna.rb +239 -0
  30. data/lib/BioDSL/commands/genecall.rb +237 -0
  31. data/lib/BioDSL/commands/grab.rb +535 -0
  32. data/lib/BioDSL/commands/index_taxonomy.rb +226 -0
  33. data/lib/BioDSL/commands/mask_seq.rb +175 -0
  34. data/lib/BioDSL/commands/mean_scores.rb +168 -0
  35. data/lib/BioDSL/commands/merge_pair_seq.rb +175 -0
  36. data/lib/BioDSL/commands/merge_table.rb +225 -0
  37. data/lib/BioDSL/commands/merge_values.rb +113 -0
  38. data/lib/BioDSL/commands/plot_heatmap.rb +233 -0
  39. data/lib/BioDSL/commands/plot_histogram.rb +306 -0
  40. data/lib/BioDSL/commands/plot_matches.rb +282 -0
  41. data/lib/BioDSL/commands/plot_residue_distribution.rb +278 -0
  42. data/lib/BioDSL/commands/plot_scores.rb +285 -0
  43. data/lib/BioDSL/commands/random.rb +153 -0
  44. data/lib/BioDSL/commands/read_fasta.rb +222 -0
  45. data/lib/BioDSL/commands/read_fastq.rb +414 -0
  46. data/lib/BioDSL/commands/read_table.rb +329 -0
  47. data/lib/BioDSL/commands/reverse_seq.rb +113 -0
  48. data/lib/BioDSL/commands/slice_align.rb +400 -0
  49. data/lib/BioDSL/commands/slice_seq.rb +151 -0
  50. data/lib/BioDSL/commands/sort.rb +223 -0
  51. data/lib/BioDSL/commands/split_pair_seq.rb +220 -0
  52. data/lib/BioDSL/commands/split_values.rb +165 -0
  53. data/lib/BioDSL/commands/trim_primer.rb +314 -0
  54. data/lib/BioDSL/commands/trim_seq.rb +192 -0
  55. data/lib/BioDSL/commands/uchime_ref.rb +170 -0
  56. data/lib/BioDSL/commands/uclust.rb +286 -0
  57. data/lib/BioDSL/commands/unique_values.rb +145 -0
  58. data/lib/BioDSL/commands/usearch_global.rb +171 -0
  59. data/lib/BioDSL/commands/usearch_local.rb +171 -0
  60. data/lib/BioDSL/commands/write_fasta.rb +207 -0
  61. data/lib/BioDSL/commands/write_fastq.rb +191 -0
  62. data/lib/BioDSL/commands/write_table.rb +419 -0
  63. data/lib/BioDSL/commands/write_tree.rb +167 -0
  64. data/lib/BioDSL/commands.rb +31 -0
  65. data/lib/BioDSL/config.rb +55 -0
  66. data/lib/BioDSL/csv.rb +307 -0
  67. data/lib/BioDSL/debug.rb +42 -0
  68. data/lib/BioDSL/fasta.rb +133 -0
  69. data/lib/BioDSL/fastq.rb +77 -0
  70. data/lib/BioDSL/filesys.rb +137 -0
  71. data/lib/BioDSL/fork.rb +145 -0
  72. data/lib/BioDSL/hamming.rb +128 -0
  73. data/lib/BioDSL/helpers/aux_helper.rb +44 -0
  74. data/lib/BioDSL/helpers/email_helper.rb +66 -0
  75. data/lib/BioDSL/helpers/history_helper.rb +40 -0
  76. data/lib/BioDSL/helpers/log_helper.rb +55 -0
  77. data/lib/BioDSL/helpers/options_helper.rb +405 -0
  78. data/lib/BioDSL/helpers/status_helper.rb +132 -0
  79. data/lib/BioDSL/helpers.rb +35 -0
  80. data/lib/BioDSL/html_report.rb +200 -0
  81. data/lib/BioDSL/math.rb +55 -0
  82. data/lib/BioDSL/mummer.rb +216 -0
  83. data/lib/BioDSL/pipeline.rb +354 -0
  84. data/lib/BioDSL/seq/ambiguity.rb +66 -0
  85. data/lib/BioDSL/seq/assemble.rb +240 -0
  86. data/lib/BioDSL/seq/backtrack.rb +252 -0
  87. data/lib/BioDSL/seq/digest.rb +99 -0
  88. data/lib/BioDSL/seq/dynamic.rb +263 -0
  89. data/lib/BioDSL/seq/homopolymer.rb +59 -0
  90. data/lib/BioDSL/seq/kmer.rb +293 -0
  91. data/lib/BioDSL/seq/levenshtein.rb +113 -0
  92. data/lib/BioDSL/seq/translate.rb +109 -0
  93. data/lib/BioDSL/seq/trim.rb +188 -0
  94. data/lib/BioDSL/seq.rb +742 -0
  95. data/lib/BioDSL/serializer.rb +98 -0
  96. data/lib/BioDSL/stream.rb +113 -0
  97. data/lib/BioDSL/taxonomy.rb +691 -0
  98. data/lib/BioDSL/test.rb +42 -0
  99. data/lib/BioDSL/tmp_dir.rb +68 -0
  100. data/lib/BioDSL/usearch.rb +301 -0
  101. data/lib/BioDSL/verbose.rb +42 -0
  102. data/lib/BioDSL/version.rb +31 -0
  103. data/lib/BioDSL.rb +81 -0
  104. data/test/BioDSL/commands/test_add_key.rb +105 -0
  105. data/test/BioDSL/commands/test_align_seq_mothur.rb +99 -0
  106. data/test/BioDSL/commands/test_analyze_residue_distribution.rb +134 -0
  107. data/test/BioDSL/commands/test_assemble_pairs.rb +459 -0
  108. data/test/BioDSL/commands/test_assemble_seq_idba.rb +50 -0
  109. data/test/BioDSL/commands/test_assemble_seq_ray.rb +51 -0
  110. data/test/BioDSL/commands/test_assemble_seq_spades.rb +50 -0
  111. data/test/BioDSL/commands/test_classify_seq.rb +50 -0
  112. data/test/BioDSL/commands/test_classify_seq_mothur.rb +59 -0
  113. data/test/BioDSL/commands/test_clip_primer.rb +377 -0
  114. data/test/BioDSL/commands/test_cluster_otus.rb +128 -0
  115. data/test/BioDSL/commands/test_collapse_otus.rb +81 -0
  116. data/test/BioDSL/commands/test_collect_otus.rb +82 -0
  117. data/test/BioDSL/commands/test_complement_seq.rb +78 -0
  118. data/test/BioDSL/commands/test_count.rb +103 -0
  119. data/test/BioDSL/commands/test_count_values.rb +85 -0
  120. data/test/BioDSL/commands/test_degap_seq.rb +96 -0
  121. data/test/BioDSL/commands/test_dereplicate_seq.rb +92 -0
  122. data/test/BioDSL/commands/test_dump.rb +109 -0
  123. data/test/BioDSL/commands/test_filter_rrna.rb +128 -0
  124. data/test/BioDSL/commands/test_genecall.rb +50 -0
  125. data/test/BioDSL/commands/test_grab.rb +398 -0
  126. data/test/BioDSL/commands/test_index_taxonomy.rb +62 -0
  127. data/test/BioDSL/commands/test_mask_seq.rb +98 -0
  128. data/test/BioDSL/commands/test_mean_scores.rb +111 -0
  129. data/test/BioDSL/commands/test_merge_pair_seq.rb +115 -0
  130. data/test/BioDSL/commands/test_merge_table.rb +131 -0
  131. data/test/BioDSL/commands/test_merge_values.rb +83 -0
  132. data/test/BioDSL/commands/test_plot_heatmap.rb +185 -0
  133. data/test/BioDSL/commands/test_plot_histogram.rb +194 -0
  134. data/test/BioDSL/commands/test_plot_matches.rb +157 -0
  135. data/test/BioDSL/commands/test_plot_residue_distribution.rb +309 -0
  136. data/test/BioDSL/commands/test_plot_scores.rb +308 -0
  137. data/test/BioDSL/commands/test_random.rb +88 -0
  138. data/test/BioDSL/commands/test_read_fasta.rb +229 -0
  139. data/test/BioDSL/commands/test_read_fastq.rb +552 -0
  140. data/test/BioDSL/commands/test_read_table.rb +327 -0
  141. data/test/BioDSL/commands/test_reverse_seq.rb +79 -0
  142. data/test/BioDSL/commands/test_slice_align.rb +218 -0
  143. data/test/BioDSL/commands/test_slice_seq.rb +131 -0
  144. data/test/BioDSL/commands/test_sort.rb +128 -0
  145. data/test/BioDSL/commands/test_split_pair_seq.rb +164 -0
  146. data/test/BioDSL/commands/test_split_values.rb +95 -0
  147. data/test/BioDSL/commands/test_trim_primer.rb +329 -0
  148. data/test/BioDSL/commands/test_trim_seq.rb +150 -0
  149. data/test/BioDSL/commands/test_uchime_ref.rb +113 -0
  150. data/test/BioDSL/commands/test_uclust.rb +139 -0
  151. data/test/BioDSL/commands/test_unique_values.rb +98 -0
  152. data/test/BioDSL/commands/test_usearch_global.rb +123 -0
  153. data/test/BioDSL/commands/test_usearch_local.rb +125 -0
  154. data/test/BioDSL/commands/test_write_fasta.rb +159 -0
  155. data/test/BioDSL/commands/test_write_fastq.rb +166 -0
  156. data/test/BioDSL/commands/test_write_table.rb +411 -0
  157. data/test/BioDSL/commands/test_write_tree.rb +122 -0
  158. data/test/BioDSL/helpers/test_options_helper.rb +272 -0
  159. data/test/BioDSL/seq/test_assemble.rb +98 -0
  160. data/test/BioDSL/seq/test_backtrack.rb +176 -0
  161. data/test/BioDSL/seq/test_digest.rb +71 -0
  162. data/test/BioDSL/seq/test_dynamic.rb +133 -0
  163. data/test/BioDSL/seq/test_homopolymer.rb +58 -0
  164. data/test/BioDSL/seq/test_kmer.rb +134 -0
  165. data/test/BioDSL/seq/test_translate.rb +75 -0
  166. data/test/BioDSL/seq/test_trim.rb +101 -0
  167. data/test/BioDSL/test_cary.rb +176 -0
  168. data/test/BioDSL/test_command.rb +45 -0
  169. data/test/BioDSL/test_csv.rb +514 -0
  170. data/test/BioDSL/test_debug.rb +42 -0
  171. data/test/BioDSL/test_fasta.rb +154 -0
  172. data/test/BioDSL/test_fastq.rb +46 -0
  173. data/test/BioDSL/test_filesys.rb +145 -0
  174. data/test/BioDSL/test_fork.rb +85 -0
  175. data/test/BioDSL/test_math.rb +41 -0
  176. data/test/BioDSL/test_mummer.rb +79 -0
  177. data/test/BioDSL/test_pipeline.rb +187 -0
  178. data/test/BioDSL/test_seq.rb +790 -0
  179. data/test/BioDSL/test_serializer.rb +72 -0
  180. data/test/BioDSL/test_stream.rb +55 -0
  181. data/test/BioDSL/test_taxonomy.rb +336 -0
  182. data/test/BioDSL/test_test.rb +42 -0
  183. data/test/BioDSL/test_tmp_dir.rb +58 -0
  184. data/test/BioDSL/test_usearch.rb +33 -0
  185. data/test/BioDSL/test_verbose.rb +42 -0
  186. data/test/helper.rb +82 -0
  187. data/www/command.html.haml +14 -0
  188. data/www/css.html.haml +55 -0
  189. data/www/input_files.html.haml +3 -0
  190. data/www/layout.html.haml +12 -0
  191. data/www/output_files.html.haml +3 -0
  192. data/www/overview.html.haml +15 -0
  193. data/www/pipeline.html.haml +4 -0
  194. data/www/png.html.haml +2 -0
  195. data/www/status.html.haml +9 -0
  196. data/www/time.html.haml +11 -0
  197. metadata +503 -0
metadata ADDED
@@ -0,0 +1,503 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: BioDSL
3
+ version: !ruby/object:Gem::Version
4
+ version: 1.0.0
5
+ platform: ruby
6
+ authors:
7
+ - Martin A. Hansen
8
+ autorequire:
9
+ bindir: bin
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+ cert_chain: []
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+ date: 2015-09-30 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
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+ name: haml
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+ requirement: !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: 4.0.5
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !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: 4.0.5
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+ - !ruby/object:Gem::Dependency
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+ name: RubyInline
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+ requirement: !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: 3.12.2
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+ type: :runtime
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+ prerelease: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 3.12.2
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+ - !ruby/object:Gem::Dependency
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+ name: narray
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+ requirements:
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+ - !ruby/object:Gem::Version
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+ version: 0.6.0
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+ requirements:
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+ - !ruby/object:Gem::Version
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+ version: 0.6.0
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+ name: mail
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+ requirements:
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+ version: 2.5.4
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 2.0.2
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+ - !ruby/object:Gem::Dependency
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+ name: terminal-table
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ version: 1.4.5
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+ name: tilt
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+ requirement: !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: 2.0.1
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !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: 2.0.1
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !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: 1.7.4
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 1.7.4
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+ - !ruby/object:Gem::Dependency
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+ name: simplecov
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+ requirement: !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: 0.9.2
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 0.9.2
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+ - !ruby/object:Gem::Dependency
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+ name: mocha
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+ requirement: !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: 1.0.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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: 1.0.0
195
+ description: BioDSL is a Bioinformatics Domain Specific Language.
196
+ email: mail@maasha.dk
197
+ executables: []
198
+ extensions: []
199
+ extra_rdoc_files: []
200
+ files:
201
+ - ".gitignore"
202
+ - BioDSL.gemspec
203
+ - LICENSE
204
+ - README.md
205
+ - Rakefile
206
+ - examples/fastq_to_fasta.rb
207
+ - lib/BioDSL.rb
208
+ - lib/BioDSL/cary.rb
209
+ - lib/BioDSL/command.rb
210
+ - lib/BioDSL/commands.rb
211
+ - lib/BioDSL/commands/add_key.rb
212
+ - lib/BioDSL/commands/align_seq_mothur.rb
213
+ - lib/BioDSL/commands/analyze_residue_distribution.rb
214
+ - lib/BioDSL/commands/assemble_pairs.rb
215
+ - lib/BioDSL/commands/assemble_seq_idba.rb
216
+ - lib/BioDSL/commands/assemble_seq_ray.rb
217
+ - lib/BioDSL/commands/assemble_seq_spades.rb
218
+ - lib/BioDSL/commands/classify_seq.rb
219
+ - lib/BioDSL/commands/classify_seq_mothur.rb
220
+ - lib/BioDSL/commands/clip_primer.rb
221
+ - lib/BioDSL/commands/cluster_otus.rb
222
+ - lib/BioDSL/commands/collapse_otus.rb
223
+ - lib/BioDSL/commands/collect_otus.rb
224
+ - lib/BioDSL/commands/complement_seq.rb
225
+ - lib/BioDSL/commands/count.rb
226
+ - lib/BioDSL/commands/count_values.rb
227
+ - lib/BioDSL/commands/degap_seq.rb
228
+ - lib/BioDSL/commands/dereplicate_seq.rb
229
+ - lib/BioDSL/commands/dump.rb
230
+ - lib/BioDSL/commands/filter_rrna.rb
231
+ - lib/BioDSL/commands/genecall.rb
232
+ - lib/BioDSL/commands/grab.rb
233
+ - lib/BioDSL/commands/index_taxonomy.rb
234
+ - lib/BioDSL/commands/mask_seq.rb
235
+ - lib/BioDSL/commands/mean_scores.rb
236
+ - lib/BioDSL/commands/merge_pair_seq.rb
237
+ - lib/BioDSL/commands/merge_table.rb
238
+ - lib/BioDSL/commands/merge_values.rb
239
+ - lib/BioDSL/commands/plot_heatmap.rb
240
+ - lib/BioDSL/commands/plot_histogram.rb
241
+ - lib/BioDSL/commands/plot_matches.rb
242
+ - lib/BioDSL/commands/plot_residue_distribution.rb
243
+ - lib/BioDSL/commands/plot_scores.rb
244
+ - lib/BioDSL/commands/random.rb
245
+ - lib/BioDSL/commands/read_fasta.rb
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350
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+ licenses:
398
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399
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421
+ - test/BioDSL/commands/test_add_key.rb
422
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423
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424
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425
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426
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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439
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440
+ - test/BioDSL/commands/test_filter_rrna.rb
441
+ - test/BioDSL/commands/test_genecall.rb
442
+ - test/BioDSL/commands/test_grab.rb
443
+ - test/BioDSL/commands/test_index_taxonomy.rb
444
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445
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446
+ - test/BioDSL/commands/test_merge_pair_seq.rb
447
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448
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449
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450
+ - test/BioDSL/commands/test_plot_histogram.rb
451
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452
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453
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454
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455
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456
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457
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458
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459
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460
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461
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462
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463
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464
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465
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466
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467
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468
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469
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470
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471
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472
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473
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474
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475
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476
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477
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478
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479
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480
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481
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482
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483
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484
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485
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486
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489
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492
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493
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494
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495
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496
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497
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499
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500
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501
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502
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503
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