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/commands/test_filter_rrna.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
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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
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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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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