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/test_mummer.rb CHANGED
@@ -23,7 +23,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
23
23
  # #
24
24
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
25
25
  # #
26
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
26
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
27
27
  # #
28
28
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
29
29
 
data/test/BioDSL/test_pipeline.rb CHANGED
@@ -23,7 +23,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
23
23
  # #
24
24
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
25
25
  # #
26
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
26
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
27
27
  # #
28
28
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
29
29
 
data/test/BioDSL/test_seq.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 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
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 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
-