BioDSL 1.0.1 → 1.0.2

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Files changed (186) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -0
  3. data/BioDSL.gemspec +1 -1
  4. data/Gemfile +6 -0
  5. data/README.md +289 -155
  6. data/Rakefile +18 -16
  7. data/lib/BioDSL.rb +1 -1
  8. data/lib/BioDSL/cary.rb +78 -53
  9. data/lib/BioDSL/command.rb +2 -2
  10. data/lib/BioDSL/commands.rb +1 -1
  11. data/lib/BioDSL/commands/add_key.rb +1 -1
  12. data/lib/BioDSL/commands/align_seq_mothur.rb +4 -4
  13. data/lib/BioDSL/commands/analyze_residue_distribution.rb +5 -5
  14. data/lib/BioDSL/commands/assemble_pairs.rb +13 -13
  15. data/lib/BioDSL/commands/assemble_seq_idba.rb +7 -9
  16. data/lib/BioDSL/commands/assemble_seq_ray.rb +13 -13
  17. data/lib/BioDSL/commands/assemble_seq_spades.rb +4 -4
  18. data/lib/BioDSL/commands/classify_seq.rb +8 -8
  19. data/lib/BioDSL/commands/classify_seq_mothur.rb +5 -5
  20. data/lib/BioDSL/commands/clip_primer.rb +7 -7
  21. data/lib/BioDSL/commands/cluster_otus.rb +5 -5
  22. data/lib/BioDSL/commands/collapse_otus.rb +2 -2
  23. data/lib/BioDSL/commands/collect_otus.rb +2 -2
  24. data/lib/BioDSL/commands/complement_seq.rb +4 -4
  25. data/lib/BioDSL/commands/count.rb +1 -1
  26. data/lib/BioDSL/commands/count_values.rb +2 -2
  27. data/lib/BioDSL/commands/degap_seq.rb +6 -7
  28. data/lib/BioDSL/commands/dereplicate_seq.rb +1 -1
  29. data/lib/BioDSL/commands/dump.rb +2 -2
  30. data/lib/BioDSL/commands/filter_rrna.rb +4 -4
  31. data/lib/BioDSL/commands/genecall.rb +7 -7
  32. data/lib/BioDSL/commands/grab.rb +1 -1
  33. data/lib/BioDSL/commands/index_taxonomy.rb +3 -3
  34. data/lib/BioDSL/commands/mask_seq.rb +4 -4
  35. data/lib/BioDSL/commands/mean_scores.rb +2 -2
  36. data/lib/BioDSL/commands/merge_pair_seq.rb +3 -3
  37. data/lib/BioDSL/commands/merge_table.rb +1 -1
  38. data/lib/BioDSL/commands/merge_values.rb +1 -1
  39. data/lib/BioDSL/commands/plot_heatmap.rb +4 -5
  40. data/lib/BioDSL/commands/plot_histogram.rb +4 -4
  41. data/lib/BioDSL/commands/plot_matches.rb +5 -5
  42. data/lib/BioDSL/commands/plot_residue_distribution.rb +6 -6
  43. data/lib/BioDSL/commands/plot_scores.rb +7 -7
  44. data/lib/BioDSL/commands/random.rb +1 -1
  45. data/lib/BioDSL/commands/read_fasta.rb +9 -9
  46. data/lib/BioDSL/commands/read_fastq.rb +16 -16
  47. data/lib/BioDSL/commands/read_table.rb +2 -3
  48. data/lib/BioDSL/commands/reverse_seq.rb +4 -4
  49. data/lib/BioDSL/commands/slice_align.rb +4 -4
  50. data/lib/BioDSL/commands/slice_seq.rb +3 -3
  51. data/lib/BioDSL/commands/sort.rb +1 -1
  52. data/lib/BioDSL/commands/split_pair_seq.rb +6 -7
  53. data/lib/BioDSL/commands/split_values.rb +2 -2
  54. data/lib/BioDSL/commands/trim_primer.rb +13 -8
  55. data/lib/BioDSL/commands/trim_seq.rb +5 -5
  56. data/lib/BioDSL/commands/uchime_ref.rb +6 -6
  57. data/lib/BioDSL/commands/uclust.rb +5 -5
  58. data/lib/BioDSL/commands/unique_values.rb +1 -1
  59. data/lib/BioDSL/commands/usearch_global.rb +2 -2
  60. data/lib/BioDSL/commands/usearch_local.rb +2 -2
  61. data/lib/BioDSL/commands/write_fasta.rb +7 -9
  62. data/lib/BioDSL/commands/write_fastq.rb +4 -4
  63. data/lib/BioDSL/commands/write_table.rb +3 -3
  64. data/lib/BioDSL/commands/write_tree.rb +2 -3
  65. data/lib/BioDSL/config.rb +2 -2
  66. data/lib/BioDSL/csv.rb +8 -10
  67. data/lib/BioDSL/debug.rb +1 -1
  68. data/lib/BioDSL/fasta.rb +54 -40
  69. data/lib/BioDSL/fastq.rb +35 -32
  70. data/lib/BioDSL/filesys.rb +56 -47
  71. data/lib/BioDSL/fork.rb +1 -1
  72. data/lib/BioDSL/hamming.rb +1 -1
  73. data/lib/BioDSL/helpers.rb +1 -1
  74. data/lib/BioDSL/helpers/aux_helper.rb +1 -1
  75. data/lib/BioDSL/helpers/email_helper.rb +1 -1
  76. data/lib/BioDSL/helpers/history_helper.rb +1 -1
  77. data/lib/BioDSL/helpers/log_helper.rb +1 -1
  78. data/lib/BioDSL/helpers/options_helper.rb +1 -1
  79. data/lib/BioDSL/helpers/status_helper.rb +1 -1
  80. data/lib/BioDSL/html_report.rb +1 -1
  81. data/lib/BioDSL/math.rb +1 -1
  82. data/lib/BioDSL/mummer.rb +1 -1
  83. data/lib/BioDSL/pipeline.rb +1 -1
  84. data/lib/BioDSL/seq.rb +240 -231
  85. data/lib/BioDSL/seq/ambiguity.rb +1 -1
  86. data/lib/BioDSL/seq/assemble.rb +1 -1
  87. data/lib/BioDSL/seq/backtrack.rb +93 -76
  88. data/lib/BioDSL/seq/digest.rb +1 -1
  89. data/lib/BioDSL/seq/dynamic.rb +43 -55
  90. data/lib/BioDSL/seq/homopolymer.rb +34 -36
  91. data/lib/BioDSL/seq/kmer.rb +67 -50
  92. data/lib/BioDSL/seq/levenshtein.rb +35 -40
  93. data/lib/BioDSL/seq/translate.rb +64 -55
  94. data/lib/BioDSL/seq/trim.rb +60 -50
  95. data/lib/BioDSL/serializer.rb +1 -1
  96. data/lib/BioDSL/stream.rb +1 -1
  97. data/lib/BioDSL/taxonomy.rb +1 -1
  98. data/lib/BioDSL/test.rb +1 -1
  99. data/lib/BioDSL/tmp_dir.rb +1 -1
  100. data/lib/BioDSL/usearch.rb +1 -1
  101. data/lib/BioDSL/verbose.rb +1 -1
  102. data/lib/BioDSL/version.rb +2 -2
  103. data/test/BioDSL/commands/test_add_key.rb +1 -1
  104. data/test/BioDSL/commands/test_align_seq_mothur.rb +1 -1
  105. data/test/BioDSL/commands/test_analyze_residue_distribution.rb +1 -1
  106. data/test/BioDSL/commands/test_assemble_pairs.rb +1 -1
  107. data/test/BioDSL/commands/test_assemble_seq_idba.rb +1 -1
  108. data/test/BioDSL/commands/test_assemble_seq_ray.rb +1 -1
  109. data/test/BioDSL/commands/test_assemble_seq_spades.rb +1 -1
  110. data/test/BioDSL/commands/test_classify_seq.rb +1 -1
  111. data/test/BioDSL/commands/test_classify_seq_mothur.rb +1 -1
  112. data/test/BioDSL/commands/test_clip_primer.rb +1 -1
  113. data/test/BioDSL/commands/test_cluster_otus.rb +1 -1
  114. data/test/BioDSL/commands/test_collapse_otus.rb +1 -1
  115. data/test/BioDSL/commands/test_collect_otus.rb +1 -1
  116. data/test/BioDSL/commands/test_complement_seq.rb +1 -1
  117. data/test/BioDSL/commands/test_count.rb +1 -1
  118. data/test/BioDSL/commands/test_count_values.rb +1 -1
  119. data/test/BioDSL/commands/test_degap_seq.rb +1 -1
  120. data/test/BioDSL/commands/test_dereplicate_seq.rb +1 -1
  121. data/test/BioDSL/commands/test_dump.rb +1 -1
  122. data/test/BioDSL/commands/test_filter_rrna.rb +1 -1
  123. data/test/BioDSL/commands/test_genecall.rb +1 -1
  124. data/test/BioDSL/commands/test_grab.rb +1 -1
  125. data/test/BioDSL/commands/test_index_taxonomy.rb +1 -1
  126. data/test/BioDSL/commands/test_mask_seq.rb +1 -1
  127. data/test/BioDSL/commands/test_mean_scores.rb +1 -1
  128. data/test/BioDSL/commands/test_merge_pair_seq.rb +1 -1
  129. data/test/BioDSL/commands/test_merge_table.rb +1 -1
  130. data/test/BioDSL/commands/test_merge_values.rb +1 -1
  131. data/test/BioDSL/commands/test_plot_heatmap.rb +1 -1
  132. data/test/BioDSL/commands/test_plot_histogram.rb +1 -1
  133. data/test/BioDSL/commands/test_plot_matches.rb +1 -1
  134. data/test/BioDSL/commands/test_plot_residue_distribution.rb +1 -1
  135. data/test/BioDSL/commands/test_plot_scores.rb +1 -1
  136. data/test/BioDSL/commands/test_random.rb +1 -1
  137. data/test/BioDSL/commands/test_read_fasta.rb +1 -1
  138. data/test/BioDSL/commands/test_read_fastq.rb +1 -1
  139. data/test/BioDSL/commands/test_read_table.rb +1 -1
  140. data/test/BioDSL/commands/test_reverse_seq.rb +1 -1
  141. data/test/BioDSL/commands/test_slice_align.rb +1 -1
  142. data/test/BioDSL/commands/test_slice_seq.rb +1 -1
  143. data/test/BioDSL/commands/test_sort.rb +1 -1
  144. data/test/BioDSL/commands/test_split_pair_seq.rb +1 -1
  145. data/test/BioDSL/commands/test_split_values.rb +1 -1
  146. data/test/BioDSL/commands/test_trim_primer.rb +1 -1
  147. data/test/BioDSL/commands/test_trim_seq.rb +1 -1
  148. data/test/BioDSL/commands/test_uchime_ref.rb +1 -1
  149. data/test/BioDSL/commands/test_uclust.rb +1 -1
  150. data/test/BioDSL/commands/test_unique_values.rb +1 -1
  151. data/test/BioDSL/commands/test_usearch_global.rb +1 -1
  152. data/test/BioDSL/commands/test_usearch_local.rb +1 -1
  153. data/test/BioDSL/commands/test_write_fasta.rb +1 -1
  154. data/test/BioDSL/commands/test_write_fastq.rb +1 -1
  155. data/test/BioDSL/commands/test_write_table.rb +1 -1
  156. data/test/BioDSL/commands/test_write_tree.rb +1 -1
  157. data/test/BioDSL/helpers/test_options_helper.rb +3 -3
  158. data/test/BioDSL/seq/test_assemble.rb +58 -56
  159. data/test/BioDSL/seq/test_backtrack.rb +83 -81
  160. data/test/BioDSL/seq/test_digest.rb +47 -45
  161. data/test/BioDSL/seq/test_dynamic.rb +66 -64
  162. data/test/BioDSL/seq/test_homopolymer.rb +35 -33
  163. data/test/BioDSL/seq/test_kmer.rb +29 -28
  164. data/test/BioDSL/seq/test_translate.rb +44 -42
  165. data/test/BioDSL/seq/test_trim.rb +59 -57
  166. data/test/BioDSL/test_cary.rb +1 -1
  167. data/test/BioDSL/test_command.rb +2 -2
  168. data/test/BioDSL/test_csv.rb +34 -31
  169. data/test/BioDSL/test_debug.rb +31 -31
  170. data/test/BioDSL/test_fasta.rb +30 -29
  171. data/test/BioDSL/test_fastq.rb +27 -26
  172. data/test/BioDSL/test_filesys.rb +28 -27
  173. data/test/BioDSL/test_fork.rb +29 -28
  174. data/test/BioDSL/test_math.rb +31 -30
  175. data/test/BioDSL/test_mummer.rb +1 -1
  176. data/test/BioDSL/test_pipeline.rb +1 -1
  177. data/test/BioDSL/test_seq.rb +42 -41
  178. data/test/BioDSL/test_serializer.rb +35 -33
  179. data/test/BioDSL/test_stream.rb +28 -27
  180. data/test/BioDSL/test_taxonomy.rb +38 -37
  181. data/test/BioDSL/test_test.rb +32 -31
  182. data/test/BioDSL/test_tmp_dir.rb +1 -1
  183. data/test/BioDSL/test_usearch.rb +28 -27
  184. data/test/BioDSL/test_verbose.rb +32 -31
  185. data/test/helper.rb +34 -31
  186. metadata +3 -2
data/test/BioDSL/test_mummer.rb CHANGED
@@ -23,7 +23,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
23
23
  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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  # #
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- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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data/test/BioDSL/test_pipeline.rb CHANGED
@@ -23,7 +23,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
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23
  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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  # #
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- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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data/test/BioDSL/test_seq.rb CHANGED
@@ -1,35 +1,36 @@
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  #!/usr/bin/env ruby
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- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
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-
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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- # #
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- # This program is free software; you can redistribute it and/or #
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- # modify it under the terms of the GNU General Public License #
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- # as published by the Free Software Foundation; either version 2 #
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- # of the License, or (at your option) any later version. #
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- # #
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- # This program is distributed in the hope that it will be useful, #
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- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
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- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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- # GNU General Public License for more details. #
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- # #
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- # You should have received a copy of the GNU General Public License #
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- # along with this program; if not, write to the Free Software #
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- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
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- # #
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- # http://www.gnu.org/copyleft/gpl.html #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # This software is part of BioDSL (www.BioDSL.org). #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
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+
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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+ # #
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+ # This program is free software; you can redistribute it and/or #
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+ # modify it under the terms of the GNU General Public License #
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+ # as published by the Free Software Foundation; either version 2 #
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+ # of the License, or (at your option) any later version. #
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+ # #
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+ # This program is distributed in the hope that it will be useful, #
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+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
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+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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+ # GNU General Public License for more details. #
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+ # #
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+ # You should have received a copy of the GNU General Public License #
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+ # along with this program; if not, write to the Free Software #
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+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
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+ # USA. #
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+ # #
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+ # http://www.gnu.org/copyleft/gpl.html #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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30
 
30
31
  require 'test/helper'
31
32
 
32
- class TestSeq < Test::Unit::TestCase
33
+ class TestSeq < Test::Unit::TestCase
33
34
  def setup
34
35
  @entry = BioDSL::Seq.new
35
36
  end
@@ -116,31 +117,31 @@ class TestSeq < Test::Unit::TestCase
116
117
  assert_nothing_raised { BioDSL::Seq.check_name_pair(entry1, entry2) }
117
118
  end
118
119
 
119
- test "#is_dna? with no sequence type returns false" do
120
- assert(@entry.is_dna? == false)
120
+ test "#dna? with no sequence type returns false" do
121
+ assert(@entry.dna? == false)
121
122
  end
122
123
 
123
- test "#is_dna? with dna sequence type returns true" do
124
+ test "#dna? with dna sequence type returns true" do
124
125
  @entry.type = :dna
125
- assert(@entry.is_dna? == true)
126
+ assert(@entry.dna? == true)
126
127
  end
127
128
 
128
- test "#is_rna? with no sequence type returns false" do
129
- assert(@entry.is_rna? == false)
129
+ test "#rna? with no sequence type returns false" do
130
+ assert(@entry.rna? == false)
130
131
  end
131
132
 
132
- test "#is_rna? with rna sequence type returns true" do
133
+ test "#rna? with rna sequence type returns true" do
133
134
  @entry.type = :rna
134
- assert(@entry.is_rna? == true)
135
+ assert(@entry.rna? == true)
135
136
  end
136
137
 
137
- test "#is_protein? with no sequence type returns false" do
138
- assert(@entry.is_protein? == false)
138
+ test "#protein? with no sequence type returns false" do
139
+ assert(@entry.protein? == false)
139
140
  end
140
141
 
141
- test "#is_protein? with protein sequence type returns true" do
142
+ test "#protein? with protein sequence type returns true" do
142
143
  @entry.type = :protein
143
- assert_equal(true, @entry.is_protein?)
144
+ assert_equal(true, @entry.protein?)
144
145
  end
145
146
 
146
147
  test "#type_guess without sequence raises" do
@@ -397,7 +398,7 @@ class TestSeq < Test::Unit::TestCase
397
398
  end
398
399
 
399
400
  test "#shuffle returns correctly" do
400
- orig = "actgactgactgatcgatcgatcgatcgtactg"
401
+ orig = "actgactgactgatcgatcgatcgatcgtactg"
401
402
  @entry.seq = "actgactgactgatcgatcgatcgatcgtactg"
402
403
  entry_shuf = @entry.shuffle
403
404
  assert_equal(orig, @entry.seq)
data/test/BioDSL/test_serializer.rb CHANGED
@@ -1,50 +1,52 @@
1
1
  #!/usr/bin/env ruby
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- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
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+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
3
3
 
4
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
- # #
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- # This program is free software; you can redistribute it and/or #
9
- # modify it under the terms of the GNU General Public License #
10
- # as published by the Free Software Foundation; either version 2 #
11
- # of the License, or (at your option) any later version. #
12
- # #
13
- # This program is distributed in the hope that it will be useful, #
14
- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
- # GNU General Public License for more details. #
17
- # #
18
- # You should have received a copy of the GNU General Public License #
19
- # along with this program; if not, write to the Free Software #
20
- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
21
- # #
22
- # http://www.gnu.org/copyleft/gpl.html #
23
- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
26
- # This software is part of BioDSL (www.BioDSL.org). #
27
- # #
28
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
+ # #
8
+ # This program is free software; you can redistribute it and/or #
9
+ # modify it under the terms of the GNU General Public License #
10
+ # as published by the Free Software Foundation; either version 2 #
11
+ # of the License, or (at your option) any later version. #
12
+ # #
13
+ # This program is distributed in the hope that it will be useful, #
14
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
+ # GNU General Public License for more details. #
17
+ # #
18
+ # You should have received a copy of the GNU General Public License #
19
+ # along with this program; if not, write to the Free Software #
20
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
21
+ # USA. #
22
+ # #
23
+ # http://www.gnu.org/copyleft/gpl.html #
24
+ # #
25
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
+ # #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
+ # #
29
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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30
 
30
31
  require 'test/helper'
31
32
 
32
- class TestSerializer < Test::Unit::TestCase
33
+ # Test class for Serializer.
34
+ class TestSerializer < Test::Unit::TestCase
33
35
  def setup
34
36
  @records = [
35
- {"foo" => 1},
36
- {"bar" => 2}
37
+ {'foo' => 1},
38
+ {'bar' => 2}
37
39
  ]
38
40
  end
39
41
 
40
- test "BioDSL::Serializer with no block raises" do
41
- assert_raise(BioDSL::SerializerError) { BioDSL::Serializer.new("foo") }
42
+ test 'BioDSL::Serializer with no block raises' do
43
+ assert_raise(BioDSL::SerializerError) { BioDSL::Serializer.new('foo') }
42
44
  end
43
45
 
44
- test "BioDSL::Serializer returns correctly" do
46
+ test 'BioDSL::Serializer returns correctly' do
45
47
  require 'tempfile'
46
48
 
47
- file = Tempfile.new("serializer")
49
+ file = Tempfile.new('serializer')
48
50
 
49
51
  begin
50
52
  File.open(file, 'wb') do |io|
data/test/BioDSL/test_stream.rb CHANGED
@@ -1,35 +1,36 @@
1
1
  #!/usr/bin/env ruby
2
- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
2
+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
3
3
 
4
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
5
- # #
6
- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
- # #
8
- # This program is free software; you can redistribute it and/or #
9
- # modify it under the terms of the GNU General Public License #
10
- # as published by the Free Software Foundation; either version 2 #
11
- # of the License, or (at your option) any later version. #
12
- # #
13
- # This program is distributed in the hope that it will be useful, #
14
- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
- # GNU General Public License for more details. #
17
- # #
18
- # You should have received a copy of the GNU General Public License #
19
- # along with this program; if not, write to the Free Software #
20
- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
21
- # #
22
- # http://www.gnu.org/copyleft/gpl.html #
23
- # #
24
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
25
- # #
26
- # This software is part of BioDSL (www.BioDSL.org). #
27
- # #
28
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
4
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
5
+ # #
6
+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
+ # #
8
+ # This program is free software; you can redistribute it and/or #
9
+ # modify it under the terms of the GNU General Public License #
10
+ # as published by the Free Software Foundation; either version 2 #
11
+ # of the License, or (at your option) any later version. #
12
+ # #
13
+ # This program is distributed in the hope that it will be useful, #
14
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
+ # GNU General Public License for more details. #
17
+ # #
18
+ # You should have received a copy of the GNU General Public License #
19
+ # along with this program; if not, write to the Free Software #
20
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
21
+ # USA. #
22
+ # #
23
+ # http://www.gnu.org/copyleft/gpl.html #
24
+ # #
25
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
+ # #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
+ # #
29
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
29
30
 
30
31
  require 'test/helper'
31
32
 
32
- class TestStream < Test::Unit::TestCase
33
+ class TestStream < Test::Unit::TestCase
33
34
  def setup
34
35
  @obj = {foo: "bar"}
35
36
  @reader, @writer = BioDSL::Stream.pipe
data/test/BioDSL/test_taxonomy.rb CHANGED
@@ -1,35 +1,36 @@
1
1
  #!/usr/bin/env ruby
2
- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
3
-
4
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
5
- # #
6
- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
- # #
8
- # This program is free software; you can redistribute it and/or #
9
- # modify it under the terms of the GNU General Public License #
10
- # as published by the Free Software Foundation; either version 2 #
11
- # of the License, or (at your option) any later version. #
12
- # #
13
- # This program is distributed in the hope that it will be useful, #
14
- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
- # GNU General Public License for more details. #
17
- # #
18
- # You should have received a copy of the GNU General Public License #
19
- # along with this program; if not, write to the Free Software #
20
- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
21
- # #
22
- # http://www.gnu.org/copyleft/gpl.html #
23
- # #
24
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
25
- # #
26
- # This software is part of BioDSL (www.BioDSL.org). #
27
- # #
28
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
2
+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
3
+
4
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
5
+ # #
6
+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
+ # #
8
+ # This program is free software; you can redistribute it and/or #
9
+ # modify it under the terms of the GNU General Public License #
10
+ # as published by the Free Software Foundation; either version 2 #
11
+ # of the License, or (at your option) any later version. #
12
+ # #
13
+ # This program is distributed in the hope that it will be useful, #
14
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
+ # GNU General Public License for more details. #
17
+ # #
18
+ # You should have received a copy of the GNU General Public License #
19
+ # along with this program; if not, write to the Free Software #
20
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
21
+ # USA. #
22
+ # #
23
+ # http://www.gnu.org/copyleft/gpl.html #
24
+ # #
25
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
+ # #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
+ # #
29
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
29
30
 
30
31
  require 'test/helper'
31
32
 
32
- class TestTaxonomy < Test::Unit::TestCase
33
+ class TestTaxonomy < Test::Unit::TestCase
33
34
  def setup
34
35
  @tmpdir = Dir.mktmpdir("Taxonomy")
35
36
 
@@ -40,7 +41,7 @@ class TestTaxonomy < Test::Unit::TestCase
40
41
  @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#f;C#;O#;F#;G#;S#", seq: "aagu"))
41
42
  @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#;C#;O#;F#;G#;S#", seq: "aag"))
42
43
  @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#g;O#;F#;G#;S#", seq: "aagag"))
43
-
44
+
44
45
  @index3 = BioDSL::Taxonomy::Index.new(kmer_size: 3, step_size: 1, output_dir: @tmpdir, prefix: "test")
45
46
  @index3.add(BioDSL::Seq.new(seq_name: "K#a;P#b;C#;O#;F#;G#;S#", seq: "aagc"))
46
47
  @index3.add(BioDSL::Seq.new(seq_name: "K#a;P#c;C#d;O#;F#;G#;S#", seq: "aagag"))
@@ -103,7 +104,7 @@ class TestTaxonomy < Test::Unit::TestCase
103
104
  assert_equal("e", @index.get_node(2).name)
104
105
  assert_equal([], @index.get_node(0).kmers.to_a)
105
106
  assert_equal([], @index.get_node(1).kmers.to_a)
106
- assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12
107
+ assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12
107
108
  end
108
109
 
109
110
  test "BioDSL::Taxonomy::Index#add with edge split returns correctly" do
@@ -116,8 +117,8 @@ class TestTaxonomy < Test::Unit::TestCase
116
117
  assert_equal("f", @index.get_node(3).name)
117
118
  assert_equal([], @index.get_node(0).kmers.to_a)
118
119
  assert_equal([], @index.get_node(1).kmers.to_a)
119
- assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12
120
- assert_equal([3, 13], @index.get_node(3).kmers.to_a) # aag=000011=3, agu=001101=13
120
+ assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12
121
+ assert_equal([3, 13], @index.get_node(3).kmers.to_a) # aag=000011=3, agu=001101=13
121
122
  end
122
123
 
123
124
  test "BioDSL::Taxonomy::Index#add to existing non-leaf node returns correctly" do
@@ -131,8 +132,8 @@ class TestTaxonomy < Test::Unit::TestCase
131
132
  assert_equal("f", @index.get_node(3).name)
132
133
  assert_equal([], @index.get_node(0).kmers.to_a)
133
134
  assert_equal([3], @index.get_node(1).kmers.to_a) # aag=000011=3
134
- assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12
135
- assert_equal([3, 13], @index.get_node(3).kmers.to_a) # aag=000011=3, agu=001101=13
135
+ assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12
136
+ assert_equal([3, 13], @index.get_node(3).kmers.to_a) # aag=000011=3, agu=001101=13
136
137
  end
137
138
 
138
139
  test "BioDSL::Taxonomy::Index#add exteding existing leaf node returns correctly" do
@@ -148,9 +149,9 @@ class TestTaxonomy < Test::Unit::TestCase
148
149
  assert_equal("g", @index.get_node(4).name)
149
150
  assert_equal([], @index.get_node(0).kmers.to_a.sort)
150
151
  assert_equal([3], @index.get_node(1).kmers.to_a.sort) # aag=000011=3
151
- assert_equal([3, 12], @index.get_node(2).kmers.to_a.sort) # aag=000011=3, aga=001100=12
152
- assert_equal([3, 13], @index.get_node(3).kmers.to_a.sort) # aag=000011=3, agu=001101=13
153
- assert_equal([3, 12, 51], @index.get_node(4).kmers.to_a.sort) # aag=000011=3, aga=001101=12, gag=110011=51
152
+ assert_equal([3, 12], @index.get_node(2).kmers.to_a.sort) # aag=000011=3, aga=001100=12
153
+ assert_equal([3, 13], @index.get_node(3).kmers.to_a.sort) # aag=000011=3, agu=001101=13
154
+ assert_equal([3, 12, 51], @index.get_node(4).kmers.to_a.sort) # aag=000011=3, aga=001101=12, gag=110011=51
154
155
  end
155
156
 
156
157
  test "BioDSL::Taxonomy::Index#tree_union returns correctly" do
data/test/BioDSL/test_test.rb CHANGED
@@ -1,42 +1,43 @@
1
1
  #!/usr/bin/env ruby
2
- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
2
+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
3
3
 
4
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
5
- # #
6
- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
- # #
8
- # This program is free software; you can redistribute it and/or #
9
- # modify it under the terms of the GNU General Public License #
10
- # as published by the Free Software Foundation; either version 2 #
11
- # of the License, or (at your option) any later version. #
12
- # #
13
- # This program is distributed in the hope that it will be useful, #
14
- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
- # GNU General Public License for more details. #
17
- # #
18
- # You should have received a copy of the GNU General Public License #
19
- # along with this program; if not, write to the Free Software #
20
- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
21
- # #
22
- # http://www.gnu.org/copyleft/gpl.html #
23
- # #
24
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
25
- # #
26
- # This software is part of BioDSL (www.BioDSL.org). #
27
- # #
28
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
4
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
5
+ # #
6
+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
7
+ # #
8
+ # This program is free software; you can redistribute it and/or #
9
+ # modify it under the terms of the GNU General Public License #
10
+ # as published by the Free Software Foundation; either version 2 #
11
+ # of the License, or (at your option) any later version. #
12
+ # #
13
+ # This program is distributed in the hope that it will be useful, #
14
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
15
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
16
+ # GNU General Public License for more details. #
17
+ # #
18
+ # You should have received a copy of the GNU General Public License #
19
+ # along with this program; if not, write to the Free Software #
20
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
21
+ # USA. #
22
+ # #
23
+ # http://www.gnu.org/copyleft/gpl.html #
24
+ # #
25
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
+ # #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
+ # #
29
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
29
30
 
30
31
  require 'test/helper'
31
32
 
33
+ # Test class for Test.
32
34
  class TestTest < Test::Unit::TestCase
33
35
  def teardown
34
- BioDSL::test = false
36
+ BioDSL.test = false
35
37
  end
36
38
 
37
- test "BioDSL::test returns correctly" do
38
- BioDSL::test = true
39
- assert_equal(true, BioDSL::test)
39
+ test 'BioDSL::test returns correctly' do
40
+ BioDSL.test = true
41
+ assert_equal(true, BioDSL.test)
40
42
  end
41
43
  end
42
-