BioDSL 1.0.1 → 1.0.2

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 (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/commands/test_filter_rrna.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
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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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data/test/BioDSL/commands/test_genecall.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
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data/test/BioDSL/commands/test_grab.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
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data/test/BioDSL/commands/test_index_taxonomy.rb CHANGED
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data/test/BioDSL/commands/test_mask_seq.rb CHANGED
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data/test/BioDSL/commands/test_mean_scores.rb CHANGED
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data/test/BioDSL/commands/test_merge_pair_seq.rb CHANGED
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data/test/BioDSL/commands/test_merge_table.rb CHANGED
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data/test/BioDSL/commands/test_merge_values.rb CHANGED
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data/test/BioDSL/commands/test_plot_heatmap.rb CHANGED
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data/test/BioDSL/commands/test_plot_histogram.rb CHANGED
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data/test/BioDSL/commands/test_plot_matches.rb CHANGED
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data/test/BioDSL/commands/test_plot_residue_distribution.rb CHANGED
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data/test/BioDSL/commands/test_plot_scores.rb CHANGED
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data/test/BioDSL/commands/test_random.rb CHANGED
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_read_fasta.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_read_fastq.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_read_table.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_reverse_seq.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_slice_align.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_slice_seq.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_sort.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_split_pair_seq.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_split_values.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_trim_primer.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_trim_seq.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_uchime_ref.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_uclust.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_unique_values.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_usearch_global.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_usearch_local.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_write_fasta.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_write_fastq.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_write_table.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/commands/test_write_tree.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
data/test/BioDSL/helpers/test_options_helper.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  # #
27
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
27
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
28
28
  # #
29
29
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
30
30
 
@@ -233,12 +233,12 @@ class TestOptionsHelper < Test::Unit::TestCase
233
233
  end
234
234
 
235
235
  test '#options_glob returns correctly' do
236
- glob = __FILE__[0..-3] + '*'
236
+ glob = __FILE__[0..-3] + '*'
237
237
  assert_equal([__FILE__], options_glob(glob))
238
238
  end
239
239
 
240
240
  test '#options_glob with Array returns correctly' do
241
- glob = __FILE__[0..-3] + '*'
241
+ glob = __FILE__[0..-3] + '*'
242
242
  assert_equal([__FILE__, __FILE__], options_glob([glob, glob]))
243
243
  end
244
244
 
data/test/BioDSL/seq/test_assemble.rb CHANGED
@@ -1,97 +1,99 @@
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 TestAssemble < Test::Unit::TestCase
33
+ # Test class for Assemble.
34
+ class TestAssemble < Test::Unit::TestCase
33
35
  def setup
34
- @entry1 = BioDSL::Seq.new(seq: "ttttttttttATCTCGC")
35
- @entry2 = BioDSL::Seq.new(seq: "naTCTCGgaaaaaaaaa")
36
+ @entry1 = BioDSL::Seq.new(seq: 'ttttttttttATCTCGC')
37
+ @entry2 = BioDSL::Seq.new(seq: 'naTCTCGgaaaaaaaaa')
36
38
  end
37
39
 
38
- test "#assemble with bad mismatches_max raises" do
40
+ test '#assemble with bad mismatches_max raises' do
39
41
  assert_raise(BioDSL::AssembleError) { BioDSL::Assemble.pair(@entry1, @entry2, mismatches_max: -1) }
40
42
  end
41
43
 
42
- test "#assemble with bad overlap_max raises" do
44
+ test '#assemble with bad overlap_max raises' do
43
45
  assert_raise(BioDSL::AssembleError) { BioDSL::Assemble.pair(@entry1, @entry2, overlap_max: 0) }
44
46
  end
45
47
 
46
- test "#assemble with bad overlap_min raises" do
48
+ test '#assemble with bad overlap_min raises' do
47
49
  assert_raise(BioDSL::AssembleError) { BioDSL::Assemble.pair(@entry1, @entry2, overlap_min: 0) }
48
50
  end
49
51
 
50
- test "#assemble returns correctly" do
52
+ test '#assemble returns correctly' do
51
53
  assembly = BioDSL::Assemble.pair(@entry1, @entry2)
52
- assert_equal("ttttttttttatctcgCatctcggaaaaaaaaa", assembly.seq)
54
+ assert_equal('ttttttttttatctcgCatctcggaaaaaaaaa', assembly.seq)
53
55
  end
54
56
 
55
- test "#assemble with uneven sequence length returns correctly" do
56
- @entry1.seq = "tttttttttATCTCGC"
57
- @entry2.seq = "naTCTCGgaaaaa"
57
+ test '#assemble with uneven sequence length returns correctly' do
58
+ @entry1.seq = 'tttttttttATCTCGC'
59
+ @entry2.seq = 'naTCTCGgaaaaa'
58
60
  assembly = BioDSL::Assemble.pair(@entry1, @entry2)
59
- assert_equal("tttttttttatctcgCatctcggaaaaa", assembly.seq)
61
+ assert_equal('tttttttttatctcgCatctcggaaaaa', assembly.seq)
60
62
  end
61
63
 
62
- test "#assemble with subsequence returns correctly" do
63
- @entry1.seq = "tttttttttATCTCGC"
64
- @entry2.seq = "naTCTCG"
64
+ test '#assemble with subsequence returns correctly' do
65
+ @entry1.seq = 'tttttttttATCTCGC'
66
+ @entry2.seq = 'naTCTCG'
65
67
  assembly = BioDSL::Assemble.pair(@entry1, @entry2)
66
- assert_equal("ttttttttTATCTCGc", assembly.seq)
68
+ assert_equal('ttttttttTATCTCGc', assembly.seq)
67
69
  end
68
70
 
69
- test "#assemble with seq_name returns correctly" do
70
- @entry1.seq_name = "foo"
71
+ test '#assemble with seq_name returns correctly' do
72
+ @entry1.seq_name = 'foo'
71
73
  assembly = BioDSL::Assemble.pair(@entry1, @entry2)
72
- assert_equal("foo:overlap=1:hamming=0", assembly.seq_name)
73
- assert_equal("ttttttttttatctcgCatctcggaaaaaaaaa", assembly.seq)
74
+ assert_equal('foo:overlap=1:hamming=0', assembly.seq_name)
75
+ assert_equal('ttttttttttatctcgCatctcggaaaaaaaaa', assembly.seq)
74
76
  end
75
77
 
76
- test "#assemble with qual returns correctly" do
77
- @entry1.qual = "00000000000000000"
78
- @entry2.qual = "@@@@@@@@@@@@@@@@@"
78
+ test '#assemble with qual returns correctly' do
79
+ @entry1.qual = '00000000000000000'
80
+ @entry2.qual = '@@@@@@@@@@@@@@@@@'
79
81
  assembly = BioDSL::Assemble.pair(@entry1, @entry2)
80
- assert_equal("ttttttttttatctcgNatctcggaaaaaaaaa", assembly.seq)
81
- assert_equal("00000000000000008@@@@@@@@@@@@@@@@", assembly.qual)
82
+ assert_equal('ttttttttttatctcgNatctcggaaaaaaaaa', assembly.seq)
83
+ assert_equal('00000000000000008@@@@@@@@@@@@@@@@', assembly.qual)
82
84
  end
83
85
 
84
- test "#assemble with mismatches_max returns correctly" do
86
+ test '#assemble with mismatches_max returns correctly' do
85
87
  assembly = BioDSL::Assemble.pair(@entry1, @entry2, mismatches_max: 10)
86
- assert_equal("tttttttttTATCTCGCaaaaaaaaa", assembly.seq)
88
+ assert_equal('tttttttttTATCTCGCaaaaaaaaa', assembly.seq)
87
89
  end
88
90
 
89
- test "#assemble with overlap_max returns correctly" do
91
+ test '#assemble with overlap_max returns correctly' do
90
92
  assembly = BioDSL::Assemble.pair(@entry1, @entry2, mismatches_max: 10, overlap_max: 7)
91
- assert_equal("ttttttttttatctcgCatctcggaaaaaaaaa", assembly.seq)
93
+ assert_equal('ttttttttttatctcgCatctcggaaaaaaaaa', assembly.seq)
92
94
  end
93
95
 
94
- test "#assemble with overlap_min returns correctly" do
96
+ test '#assemble with overlap_min returns correctly' do
95
97
  assembly = BioDSL::Assemble.pair(@entry1, @entry2, mismatches_max: 10, overlap_min: 9)
96
98
  assert_nil(assembly)
97
99
  end