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/lib/BioDSL/seq/trim.rb CHANGED
@@ -1,28 +1,29 @@
1
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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- # #
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- # This program is free software; you can redistribute it and/or #
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- # modify it under the terms of the GNU General Public License #
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- # as published by the Free Software Foundation; either version 2 #
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- # of the License, or (at your option) any later version. #
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- # #
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- # This program is distributed in the hope that it will be useful, #
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- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
12
- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
13
- # GNU General Public License for more details. #
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- # #
15
- # You should have received a copy of the GNU General Public License #
16
- # along with this program; if not, write to the Free Software #
17
- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
18
- # #
19
- # http://www.gnu.org/copyleft/gpl.html #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
23
- # This software is part of BioDSL (www.BioDSL.org). #
24
- # #
25
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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+ # #
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+ # This program is free software; you can redistribute it and/or #
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+ # modify it under the terms of the GNU General Public License #
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+ # as published by the Free Software Foundation; either version 2 #
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+ # of the License, or (at your option) any later version. #
9
+ # #
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+ # This program is distributed in the hope that it will be useful, #
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+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
12
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
13
+ # GNU General Public License for more details. #
14
+ # #
15
+ # You should have received a copy of the GNU General Public License #
16
+ # along with this program; if not, write to the Free Software #
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+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
18
+ # USA. #
19
+ # #
20
+ # http://www.gnu.org/copyleft/gpl.html #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # This software is part of BioDSL (www.BioDSL.org). #
25
+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
27
 
27
28
  module BioDSL
28
29
  # Error class for all exceptions to do with Trim.
@@ -31,41 +32,45 @@ module BioDSL
31
32
  # Module containing methods for end trimming sequences with suboptimal quality
32
33
  # scores.
33
34
  module Trim
34
- # Method to progressively trim a Seq object sequence from the right end until
35
- # a run of min_len residues with quality scores above min_qual is encountered.
35
+ # Method to progressively trim a Seq object sequence from the right end
36
+ # until a run of min_len residues with quality scores above min_qual is
37
+ # encountered.
36
38
  def quality_trim_right(min_qual, min_len = 1)
37
39
  check_trim_args(min_qual, min_len)
38
40
 
39
- pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
41
+ pos = trim_right_pos_c(@qual, length, min_qual, min_len, Seq::SCORE_BASE)
40
42
 
41
- self[0 .. pos]
43
+ self[0..pos]
42
44
  end
43
45
 
44
- # Method to progressively trim a Seq object sequence from the right end until
45
- # a run of min_len residues with quality scores above min_qual is encountered.
46
+ # Method to progressively trim a Seq object sequence from the right end
47
+ # until a run of min_len residues with quality scores above min_qual is
48
+ # encountered.
46
49
  def quality_trim_right!(min_qual, min_len = 1)
47
50
  subseq = quality_trim_right(min_qual, min_len)
48
51
  self.seq = subseq.seq
49
- self.qual = subseq.qual
52
+ @qual = subseq.qual
50
53
  self
51
54
  end
52
55
 
53
56
  # Method to progressively trim a Seq object sequence from the left end until
54
- # a run of min_len residues with quality scores above min_qual is encountered.
57
+ # a run of min_len residues with quality scores above min_qual is
58
+ # encountered.
55
59
  def quality_trim_left(min_qual, min_len = 1)
56
60
  check_trim_args(min_qual, min_len)
57
61
 
58
- pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
62
+ pos = trim_left_pos_c(@qual, length, min_qual, min_len, Seq::SCORE_BASE)
59
63
 
60
- self[pos .. self.length]
64
+ self[pos..length]
61
65
  end
62
66
 
63
67
  # Method to progressively trim a Seq object sequence from the left end until
64
- # a run of min_len residues with quality scores above min_qual is encountered.
68
+ # a run of min_len residues with quality scores above min_qual is
69
+ # encountered.
65
70
  def quality_trim_left!(min_qual, min_len = 1)
66
71
  subseq = quality_trim_left(min_qual, min_len)
67
72
  self.seq = subseq.seq
68
- self.qual = subseq.qual
73
+ @qual = subseq.qual
69
74
  self
70
75
  end
71
76
 
@@ -74,12 +79,14 @@ module BioDSL
74
79
  def quality_trim(min_qual, min_len = 1)
75
80
  check_trim_args(min_qual, min_len)
76
81
 
77
- pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
78
- pos_left = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
82
+ pos_right = trim_right_pos_c(@qual, length, min_qual, min_len,
83
+ Seq::SCORE_BASE)
84
+ pos_left = trim_left_pos_c(@qual, length, min_qual, min_len,
85
+ Seq::SCORE_BASE)
79
86
 
80
87
  pos_left = pos_right if pos_left > pos_right
81
88
 
82
- self[pos_left ... pos_right]
89
+ self[pos_left...pos_right]
83
90
  end
84
91
 
85
92
  # Method to progressively trim a Seq object sequence from both ends until a
@@ -87,21 +94,24 @@ module BioDSL
87
94
  def quality_trim!(min_qual, min_len = 1)
88
95
  subseq = quality_trim(min_qual, min_len)
89
96
  self.seq = subseq.seq
90
- self.qual = subseq.qual
97
+ @qual = subseq.qual
91
98
  self
92
99
  end
93
100
 
94
101
  private
95
102
 
96
- # Method to check the arguments for trimming and raise on bad sequence, qualities,
97
- # and min_qual.
103
+ # Method to check the arguments for trimming and raise on bad sequence,
104
+ # qualities, and min_qual.
98
105
  def check_trim_args(min_qual, min_len)
99
- raise TrimError, "no sequence" if self.seq.nil?
100
- raise TrimError, "no quality score" if self.qual.nil?
101
- unless (Seq::SCORE_MIN .. Seq::SCORE_MAX).include? min_qual
102
- raise TrimError, "minimum quality value: #{min_qual} out of range #{Seq::SCORE_MIN} .. #{Seq::SCORE_MAX}"
106
+ fail TrimError, 'no sequence' if @seq.nil?
107
+ fail TrimError, 'no quality score' if @qual.nil?
108
+
109
+ unless (Seq::SCORE_MIN..Seq::SCORE_MAX).include? min_qual
110
+ fail TrimError, "minimum quality value: #{min_qual} out of range: " \
111
+ "#{Seq::SCORE_MIN} .. #{Seq::SCORE_MAX}"
103
112
  end
104
- raise TrimError, "min_len must be larger than zero" if min_len <= 0
113
+
114
+ fail TrimError, 'min_len must be larger than zero' if min_len <= 0
105
115
  end
106
116
 
107
117
  # Inline C functions for speed below.
@@ -115,7 +125,7 @@ module BioDSL
115
125
  VALUE _min_len, // minimum quality length
116
126
  VALUE _score_base // score base
117
127
  )
118
- {
128
+ {
119
129
  char *qual = StringValuePtr(_qual);
120
130
  unsigned int len = FIX2UINT(_len);
121
131
  unsigned int min_qual = FIX2UINT(_min_qual);
@@ -153,7 +163,7 @@ module BioDSL
153
163
  VALUE _min_len, // minimum quality length
154
164
  VALUE _score_base // score base
155
165
  )
156
- {
166
+ {
157
167
  char *qual = StringValuePtr(_qual);
158
168
  unsigned int len = FIX2UINT(_len);
159
169
  unsigned int min_qual = FIX2UINT(_min_qual);
data/lib/BioDSL/serializer.rb CHANGED
@@ -21,7 +21,7 @@
21
21
  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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  # #
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- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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25
  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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data/lib/BioDSL/stream.rb CHANGED
@@ -21,7 +21,7 @@
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21
  # #
22
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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  # #
24
- # 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). #
25
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  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
27
27
 
data/lib/BioDSL/taxonomy.rb CHANGED
@@ -21,7 +21,7 @@
21
21
  # #
22
22
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
23
23
  # #
24
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
24
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
25
25
  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
27
27
 
data/lib/BioDSL/test.rb CHANGED
@@ -21,7 +21,7 @@
21
21
  # #
22
22
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
23
23
  # #
24
- # This software is part of the BioDSL framework (www.BioDSL.org). #
24
+ # This software is part of the BioDSL (www.BioDSL.org). #
25
25
  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
27
27
 
data/lib/BioDSL/tmp_dir.rb CHANGED
@@ -20,7 +20,7 @@
20
20
  # #
21
21
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
22
22
  # #
23
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
23
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
24
24
  # #
25
25
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
26
  module BioDSL
data/lib/BioDSL/usearch.rb CHANGED
@@ -21,7 +21,7 @@
21
21
  # #
22
22
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
23
23
  # #
24
- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
24
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
25
25
  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
27
27
 
data/lib/BioDSL/verbose.rb CHANGED
@@ -21,7 +21,7 @@
21
21
  # #
22
22
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
23
23
  # #
24
- # This software is part of the BioDSL framework (www.BioDSL.org). #
24
+ # This software is part of the BioDSL (www.BioDSL.org). #
25
25
  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
27
27
 
data/lib/BioDSL/version.rb CHANGED
@@ -21,11 +21,11 @@
21
21
  # #
22
22
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
23
23
  # #
24
- # This software is part of the BioDSL framework (www.BioDSL.org). #
24
+ # This software is part of the BioDSL (www.BioDSL.org). #
25
25
  # #
26
26
  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
27
27
 
28
28
  # Namespace for BioDSL.
29
29
  module BioDSL
30
- VERSION = '1.0.1'
30
+ VERSION = '1.0.2'
31
31
  end
data/test/BioDSL/commands/test_add_key.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_align_seq_mothur.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_analyze_residue_distribution.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_assemble_pairs.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_assemble_seq_idba.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_assemble_seq_ray.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_assemble_seq_spades.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_classify_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_classify_seq_mothur.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_clip_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_cluster_otus.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_collapse_otus.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_collect_otus.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_complement_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_count.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_count_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_degap_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_dereplicate_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_dump.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