BioDSL 1.0.1 → 1.0.2

Sign up to get free protection for your applications and to get access to all the features.
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/seq/test_homopolymer.rb CHANGED
@@ -1,56 +1,58 @@
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 TestHomopolymer < Test::Unit::TestCase
33
+ # Test class for Homopolymer.
34
+ class TestHomopolymer < Test::Unit::TestCase
33
35
  def setup
34
- @entry = BioDSL::Seq.new(seq: "atcgatTTTTTTcggttga")
36
+ @entry = BioDSL::Seq.new(seq: 'atcgatTTTTTTcggttga')
35
37
  end
36
38
 
37
- test "#each_homopolymer with bad min raises" do
39
+ test '#each_homopolymer with bad min raises' do
38
40
  assert_raise(BioDSL::HomopolymerError) { @entry.each_homopolymer(0) }
39
41
  assert_raise(BioDSL::HomopolymerError) { @entry.each_homopolymer(-1) }
40
42
  end
41
43
 
42
- test "#each_homopolymer returns correctly" do
44
+ test '#each_homopolymer returns correctly' do
43
45
  hps = @entry.each_homopolymer(3)
44
46
  assert_equal(1, hps.size)
45
47
  assert_equal(7, hps.first.length)
46
- assert_equal("TTTTTTT", hps.first.pattern)
48
+ assert_equal('TTTTTTT', hps.first.pattern)
47
49
  assert_equal(5, hps.first.pos)
48
50
  end
49
51
 
50
- test "#each_homopolymer in block context returns correctly" do
52
+ test '#each_homopolymer in block context returns correctly' do
51
53
  @entry.each_homopolymer(3) do |hp|
52
54
  assert_equal(7, hp.length)
53
- assert_equal("TTTTTTT", hp.pattern)
55
+ assert_equal('TTTTTTT', hp.pattern)
54
56
  assert_equal(5, hp.pos)
55
57
  break
56
58
  end
data/test/BioDSL/seq/test_kmer.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 TestKmer < Test::Unit::TestCase
33
+ class TestKmer < Test::Unit::TestCase
33
34
  def setup
34
35
  @entry = BioDSL::Seq.new(seq: "aNacCGactGAtacACGTAC")
35
36
  end
data/test/BioDSL/seq/test_translate.rb CHANGED
@@ -1,75 +1,77 @@
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 TestTranslate < Test::Unit::TestCase
33
+ # Test class for Translate.
34
+ class TestTranslate < Test::Unit::TestCase
33
35
  def setup
34
- @entry = BioDSL::Seq.new(seq: "atcgatcgatcgtacggttga", type: :dna)
36
+ @entry = BioDSL::Seq.new(seq: 'atcgatcgatcgtacggttga', type: :dna)
35
37
  end
36
38
 
37
- test "#tranlate with bad type raises" do
39
+ test '#tranlate with bad type raises' do
38
40
  @entry.type = nil
39
41
  assert_raise(BioDSL::SeqError) { @entry.translate }
40
42
  end
41
43
 
42
- test "#tranlate with bad length raises" do
43
- @entry.seq = "atcgatcgatcgtacggtga"
44
+ test '#tranlate with bad length raises' do
45
+ @entry.seq = 'atcgatcgatcgtacggtga'
44
46
  assert_raise(BioDSL::SeqError) { @entry.translate }
45
47
  end
46
48
 
47
- test "#tranlate with bad translation table raises" do
48
- @entry.seq = "atcgatcgatcgtacggttga"
49
+ test '#tranlate with bad translation table raises' do
50
+ @entry.seq = 'atcgatcgatcgtacggttga'
49
51
  assert_raise(BioDSL::SeqError) { @entry.translate(0) }
50
52
  end
51
53
 
52
- test "#tranlate with bad start codon raises" do
53
- @entry.seq = "ttagatcgatcgtacggttga"
54
+ test '#tranlate with bad start codon raises' do
55
+ @entry.seq = 'ttagatcgatcgtacggttga'
54
56
  assert_raise(BioDSL::SeqError) { @entry.translate }
55
57
  end
56
58
 
57
- test "#tranlate with bad codon raises" do
58
- @entry.seq = "atggatcgaxxxtcgtacggttga"
59
+ test '#tranlate with bad codon raises' do
60
+ @entry.seq = 'atggatcgaxxxtcgtacggttga'
59
61
  assert_raise(BioDSL::SeqError) { @entry.translate }
60
62
  end
61
63
 
62
- test "#tranlate returns correctly" do
64
+ test '#tranlate returns correctly' do
63
65
  entry = @entry.translate
64
- assert_equal("MDRSYG", entry.seq)
66
+ assert_equal('MDRSYG', entry.seq)
65
67
  assert_equal(:protein, entry.type)
66
- assert_equal("atcgatcgatcgtacggttga", @entry.seq)
68
+ assert_equal('atcgatcgatcgtacggttga', @entry.seq)
67
69
  assert_equal(:dna, @entry.type)
68
70
  end
69
71
 
70
- test "#tranlate! returns correctly" do
72
+ test '#tranlate! returns correctly' do
71
73
  @entry.translate!
72
- assert_equal("MDRSYG", @entry.seq)
74
+ assert_equal('MDRSYG', @entry.seq)
73
75
  assert_equal(:protein, @entry.type)
74
76
  end
75
77
  end
data/test/BioDSL/seq/test_trim.rb CHANGED
@@ -1,101 +1,103 @@
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 TestTrim < Test::Unit::TestCase
33
+ # Test class for Trim.
34
+ class TestTrim < Test::Unit::TestCase
33
35
  def setup
34
36
  @entry = BioDSL::Seq.new
35
37
  # 2 3 44 3 2
36
38
  # 8901234567890123456789009876543210987654321098
37
- @entry.qual = "3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543"
38
- @entry.seq = "abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba"
39
+ @entry.qual = '3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543'
40
+ @entry.seq = 'abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba'
39
41
  end
40
42
 
41
- test "#quality_trim with nil seq raises" do
43
+ test '#quality_trim with nil seq raises' do
42
44
  @entry.seq = nil
43
45
  assert_raise(BioDSL::TrimError) { @entry.quality_trim(20, 1) }
44
46
  end
45
47
 
46
- test "#quality_trim with nil qual raises" do
48
+ test '#quality_trim with nil qual raises' do
47
49
  @entry.qual = nil
48
50
  assert_raise(BioDSL::TrimError) { @entry.quality_trim(20, 1) }
49
51
  end
50
52
 
51
- test "#quality_trim with bad min_qual raises" do
53
+ test '#quality_trim with bad min_qual raises' do
52
54
  assert_raise(BioDSL::TrimError) { @entry.quality_trim(-1, 1) }
53
55
  assert_raise(BioDSL::TrimError) { @entry.quality_trim(41, 1) }
54
56
  end
55
57
 
56
- test "#quality_trim with bad min_len raises" do
58
+ test '#quality_trim with bad min_len raises' do
57
59
  assert_raise(BioDSL::TrimError) { @entry.quality_trim(20, 0) }
58
60
  end
59
61
 
60
- test "#quality_trim returns correctly" do
62
+ test '#quality_trim returns correctly' do
61
63
  trimmed = @entry.quality_trim(30, 3)
62
- assert_equal("pqrstuvxxvutsrqp", trimmed.seq)
63
- assert_equal("BCDEFGHIIHGFEDCB", trimmed.qual)
64
- assert_equal("abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba", @entry.seq)
65
- assert_equal("3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543", @entry.qual)
64
+ assert_equal('pqrstuvxxvutsrqp', trimmed.seq)
65
+ assert_equal('BCDEFGHIIHGFEDCB', trimmed.qual)
66
+ assert_equal('abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba', @entry.seq)
67
+ assert_equal('3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543', @entry.qual)
66
68
  end
67
69
 
68
- test "#quality_trim! returns correctly" do
70
+ test '#quality_trim! returns correctly' do
69
71
  @entry.quality_trim!(30, 3)
70
- assert_equal("pqrstuvxxvutsrqp", @entry.seq)
71
- assert_equal("BCDEFGHIIHGFEDCB", @entry.qual)
72
+ assert_equal('pqrstuvxxvutsrqp', @entry.seq)
73
+ assert_equal('BCDEFGHIIHGFEDCB', @entry.qual)
72
74
  end
73
75
 
74
- test "#quality_trim_left returns correctly" do
76
+ test '#quality_trim_left returns correctly' do
75
77
  trimmed = @entry.quality_trim_left(30, 3)
76
- assert_equal("pqrstuvxxvutsrqponmlkjihgfedcba", trimmed.seq)
77
- assert_equal("BCDEFGHIIHGFEDCB3@?>=<;:9876543", trimmed.qual)
78
- assert_equal("abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba", @entry.seq)
79
- assert_equal("3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543", @entry.qual)
78
+ assert_equal('pqrstuvxxvutsrqponmlkjihgfedcba', trimmed.seq)
79
+ assert_equal('BCDEFGHIIHGFEDCB3@?>=<;:9876543', trimmed.qual)
80
+ assert_equal('abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba', @entry.seq)
81
+ assert_equal('3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543', @entry.qual)
80
82
  end
81
83
 
82
- test "#quality_trim_left! returns correctly" do
84
+ test '#quality_trim_left! returns correctly' do
83
85
  @entry.quality_trim_left!(30, 3)
84
- assert_equal("pqrstuvxxvutsrqponmlkjihgfedcba", @entry.seq)
85
- assert_equal("BCDEFGHIIHGFEDCB3@?>=<;:9876543", @entry.qual)
86
+ assert_equal('pqrstuvxxvutsrqponmlkjihgfedcba', @entry.seq)
87
+ assert_equal('BCDEFGHIIHGFEDCB3@?>=<;:9876543', @entry.qual)
86
88
  end
87
89
 
88
- test "#quality_trim_rigth returns correctly" do
90
+ test '#quality_trim_rigth returns correctly' do
89
91
  trimmed = @entry.quality_trim_right(30, 3)
90
- assert_equal("abcdefghijklmnopqrstuvxxvutsrqpo", trimmed.seq)
91
- assert_equal("3456789:;<=>?@3BCDEFGHIIHGFEDCB3", trimmed.qual)
92
- assert_equal("abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba", @entry.seq)
93
- assert_equal("3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543", @entry.qual)
92
+ assert_equal('abcdefghijklmnopqrstuvxxvutsrqpo', trimmed.seq)
93
+ assert_equal('3456789:;<=>?@3BCDEFGHIIHGFEDCB3', trimmed.qual)
94
+ assert_equal('abcdefghijklmnopqrstuvxxvutsrqponmlkjihgfedcba', @entry.seq)
95
+ assert_equal('3456789:;<=>?@3BCDEFGHIIHGFEDCB3@?>=<;:9876543', @entry.qual)
94
96
  end
95
97
 
96
- test "#quality_trim_right! returns correctly" do
98
+ test '#quality_trim_right! returns correctly' do
97
99
  @entry.quality_trim_right!(30, 3)
98
- assert_equal("abcdefghijklmnopqrstuvxxvutsrqpo", @entry.seq)
99
- assert_equal("3456789:;<=>?@3BCDEFGHIIHGFEDCB3", @entry.qual)
100
+ assert_equal('abcdefghijklmnopqrstuvxxvutsrqpo', @entry.seq)
101
+ assert_equal('3456789:;<=>?@3BCDEFGHIIHGFEDCB3', @entry.qual)
100
102
  end
101
103
  end
data/test/BioDSL/test_cary.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/test_command.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
 
@@ -33,7 +33,7 @@ require 'test/helper'
33
33
  class CommandTest < Test::Unit::TestCase
34
34
  test 'BioDSL::Command#to_s w/o options returns OK' do
35
35
  command = BioDSL::Command.new('dump', nil, {})
36
- expected = %{dump}
36
+ expected = %(dump)
37
37
  assert_equal(expected, command.to_s)
38
38
  end
39
39