mgnu 2.1.1

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 (59) hide show
  1. checksums.yaml +7 -0
  2. data/.yardopts +0 -0
  3. data/README.md +31 -0
  4. data/Rakefile +33 -0
  5. data/lib/mgnu.rb +9 -0
  6. data/lib/mgnu/alignment.rb +143 -0
  7. data/lib/mgnu/common.rb +68 -0
  8. data/lib/mgnu/genbank.rb +117 -0
  9. data/lib/mgnu/genbank/feature.rb +84 -0
  10. data/lib/mgnu/genbank/location.rb +150 -0
  11. data/lib/mgnu/genbank/qualifier.rb +45 -0
  12. data/lib/mgnu/genbank/reference.rb +114 -0
  13. data/lib/mgnu/genbank/source.rb +39 -0
  14. data/lib/mgnu/loggable.rb +61 -0
  15. data/lib/mgnu/parser.rb +50 -0
  16. data/lib/mgnu/parser/blast.rb +87 -0
  17. data/lib/mgnu/parser/blast/format0.rb +290 -0
  18. data/lib/mgnu/parser/blast/format7.rb +121 -0
  19. data/lib/mgnu/parser/blast/format8.rb +120 -0
  20. data/lib/mgnu/parser/blast/hsp.rb +75 -0
  21. data/lib/mgnu/parser/blast/query.rb +45 -0
  22. data/lib/mgnu/parser/blast/sbjct.rb +62 -0
  23. data/lib/mgnu/parser/clustalw.rb +72 -0
  24. data/lib/mgnu/parser/fasta.rb +61 -0
  25. data/lib/mgnu/parser/fasta_header_index.rb +39 -0
  26. data/lib/mgnu/parser/fasta_index.rb +57 -0
  27. data/lib/mgnu/parser/fastq.rb +61 -0
  28. data/lib/mgnu/parser/genbank.rb +187 -0
  29. data/lib/mgnu/parser/gff.rb +56 -0
  30. data/lib/mgnu/parser/iprscan/hit.rb +76 -0
  31. data/lib/mgnu/parser/iprscan_file.rb +39 -0
  32. data/lib/mgnu/parser/kegg_ontology_index.rb +163 -0
  33. data/lib/mgnu/parser/pilercr.rb +102 -0
  34. data/lib/mgnu/parser/prodigal.rb +170 -0
  35. data/lib/mgnu/parser/sam.rb +115 -0
  36. data/lib/mgnu/parser/sam/alignment.rb +22 -0
  37. data/lib/mgnu/parser/sam/header.rb +23 -0
  38. data/lib/mgnu/parser/sam/pair.rb +18 -0
  39. data/lib/mgnu/sequence.rb +207 -0
  40. data/lib/mgnu/sequence/fasta.rb +79 -0
  41. data/lib/mgnu/sequence/fastq.rb +43 -0
  42. data/lib/mgnu/version.rb +16 -0
  43. data/mgnu.gemspec +39 -0
  44. data/spec/mgnu/parser/blast_format0_spec.rb +114 -0
  45. data/spec/mgnu/parser/blast_format7_spec.rb +24 -0
  46. data/spec/mgnu/parser/blast_format8_spec.rb +26 -0
  47. data/spec/mgnu/parser/blast_multihsp_spec.rb +100 -0
  48. data/spec/mgnu/parser/blast_oof_spec.rb +53 -0
  49. data/spec/mgnu/parser/clustalw_spec.rb +90 -0
  50. data/spec/mgnu/parser/fasta_header_index_tc_parser_spec.rb +25 -0
  51. data/spec/mgnu/parser/fasta_index_tc_parser_spec.rb +25 -0
  52. data/spec/mgnu/parser/fasta_parser_spec.rb +53 -0
  53. data/spec/mgnu/parser_spec.rb +22 -0
  54. data/spec/mgnu/sequence/fasta_spec.rb +60 -0
  55. data/spec/mgnu/sequence/fastq_spec.rb +31 -0
  56. data/spec/mgnu/sequence_spec.rb +81 -0
  57. data/spec/mgnu_spec.rb +7 -0
  58. data/spec/spec_helper.rb +53 -0
  59. metadata +376 -0
@@ -0,0 +1,53 @@
1
+ require 'spec_helper'
2
+
3
+ describe MgNu::Parser::Fasta do
4
+ before do
5
+ @ff = MgNu::Parser::Fasta.new('data/test.fasta')
6
+ end
7
+
8
+ it 'should be know about attributes' do
9
+ expect(@ff).to be_a(MgNu::Parser::Fasta)
10
+ expect(@ff).to respond_to(:filename)
11
+ expect(@ff).to respond_to(:each)
12
+ end
13
+
14
+ it 'should yield MgNu::Sequence::Fasta objects' do
15
+ count = 0
16
+ @ff.each do |f|
17
+ expect(f).to be_a(MgNu::Sequence::Fasta)
18
+ expect(f.sequence).not_to be_nil
19
+ expect(f.header).not_to be_nil
20
+ count += 1
21
+ end
22
+ expect(count).to eq(2)
23
+ end
24
+
25
+ it 'should concatenate multiline seqeunces' do
26
+ @ff.each do |f|
27
+ expect(f.sequence).not_to match(/\n/)
28
+ end
29
+ end
30
+ end
31
+
32
+ describe 'MgNu::Parser::Fasta with a fasta quality file' do
33
+ before do
34
+ @ff = MgNu::Parser::Fasta.new('data/testqual.fasta.qual', true)
35
+ end
36
+
37
+ it 'should correctly format quality strings' do
38
+ @ff.each do |f|
39
+ expect(f).to be_a(MgNu::Sequence::Fasta)
40
+ expect(f).to respond_to(:header)
41
+ expect(f).to respond_to(:sequence)
42
+ expect(f.sequence).not_to be_nil
43
+ expect(f.header).not_to be_nil
44
+ str = f.to_s
45
+ temp = str.split(/\n/)
46
+ temp.shift # drop header line
47
+
48
+ temp.each do |qline|
49
+ expect(qline.split(/\s+/).length).to eq(17)
50
+ end
51
+ end
52
+ end
53
+ end
@@ -0,0 +1,22 @@
1
+ require 'spec_helper'
2
+
3
+ describe MgNu::Parser do
4
+ class DummyClass
5
+ include MgNu::Loggable
6
+ include MgNu::Parser
7
+ end
8
+
9
+ before(:each) do
10
+ @dummy_class = DummyClass.new
11
+ @dummy_class.extend(MgNu::Parser)
12
+ end
13
+
14
+ it 'can be included' do
15
+ expect(@dummy_class).to respond_to(:parse_until)
16
+ expect(@dummy_class).to respond_to(:strip_quotes)
17
+ end
18
+
19
+ it 'can strip quotes' do
20
+ expect(@dummy_class.strip_quotes('"ABC"')).to eq('ABC')
21
+ end
22
+ end
@@ -0,0 +1,60 @@
1
+ require 'spec_helper'
2
+
3
+ describe MgNu::Sequence::Fasta do
4
+ before do
5
+ @fs = MgNu::Sequence::Fasta.new(:header => 'test', :sequence => 'atgcatgcatgcatgcaaaa')
6
+ end
7
+
8
+ it 'knows about attributes' do
9
+ expect(@fs).to be_a(MgNu::Sequence::Fasta)
10
+ expect(@fs).to respond_to(:value)
11
+ expect(@fs).to respond_to(:sequence)
12
+ expect(@fs).to respond_to(:type)
13
+ expect(@fs).to respond_to(:reverse_complement)
14
+ expect(@fs).to respond_to(:translate)
15
+ expect(@fs).to respond_to(:levenshtein_distance)
16
+ expect(@fs).to respond_to(:distance)
17
+ expect(@fs).to respond_to(:percent_identity)
18
+ expect(@fs).to respond_to(:identity)
19
+ end
20
+
21
+ it 'can represent itself as a string' do
22
+ expect(@fs.to_s).to eq(">test\natgcatgcatgcatgcaaaa")
23
+
24
+ # create a long sequence
25
+ @fs.sequence << 'atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa'
26
+
27
+ # fasta entry with 60 (the default) chars/row
28
+ result = ">test\n"
29
+ result << "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa\n"
30
+ result << "atgcatgcatgcatgcaaaaatgcatgatgcatgcatgcatgcaaaaatgcatgcatgca\n"
31
+ result << "tgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa\n"
32
+ expect(@fs.to_s).to eq(result)
33
+
34
+ # create a fasta entry with 50 chars/row
35
+ result = ">test\n"
36
+ result << "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcat\n"
37
+ result << "gcatgcaaaaatgcatgcatgcatgcaaaaatgcatgatgcatgcatgca\n"
38
+ result << "tgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatg\n"
39
+ result << "catgcatgcatgcaaaa\n"
40
+ expect(@fs.to_s(50)).to eq(result)
41
+ end
42
+
43
+ it 'can revcomp' do
44
+ expect(@fs.reverse_complement).to eq('ttttgcatgcatgcatgcat')
45
+ end
46
+
47
+ it 'cat split on N' do
48
+ fs = MgNu::Sequence::Fasta.new(
49
+ :header => 'test',
50
+ :sequence => 'atgcatgcatgcatgcaaaaNNNNNNNNNNNNNNNNNNNNNNatgcatgcatgcatgcaaaa'
51
+ )
52
+ expect(fs.split_on_n.split("\n>").length).to eq(2)
53
+
54
+ fs = MgNu::Sequence::Fasta.new(
55
+ :header => 'test',
56
+ :sequence => 'atgcatgcatgcatgcaaaannnnnnnnnnnnnnnnnnnnnnatgcatgcatgcatgcaaaa'
57
+ )
58
+ expect(fs.split_on_n.split("\n>").length).to eq(2)
59
+ end
60
+ end
@@ -0,0 +1,31 @@
1
+ require 'spec_helper'
2
+ describe MgNu::Sequence::Fastq do
3
+ before do
4
+ @fs = MgNu::Sequence::Fastq.new(
5
+ :header => 'HWI-EAS385_0092_FC:5:1:2510:1094#0/1',
6
+ :sequence => 'CAAAGGTGATTCATTTAACTGGCAATCNNNNNNNCGACCGTCGTTTTTTGTGCCT',
7
+ :quality => 'eWddWa`cbeffff__afff_ggggWWBBBBBBBUXW\YZcffbef_fbcZZa^^'
8
+ )
9
+ end
10
+
11
+ it 'knows about attributes' do
12
+ expect(@fs).to be_a(MgNu::Sequence::Fastq)
13
+ expect(@fs).to respond_to(:value)
14
+ expect(@fs).to respond_to(:value=)
15
+ expect(@fs).to respond_to(:sequence)
16
+ expect(@fs).to respond_to(:sequence=)
17
+ expect(@fs).to respond_to(:qualhdr)
18
+ expect(@fs).to respond_to(:quality)
19
+ expect(@fs).to respond_to(:unpack_quality)
20
+ end
21
+
22
+ it 'can represent itself as a string' do
23
+ result = <<EOT
24
+ @HWI-EAS385_0092_FC:5:1:2510:1094#0/1
25
+ CAAAGGTGATTCATTTAACTGGCAATCNNNNNNNCGACCGTCGTTTTTTGTGCCT
26
+ +
27
+ eWddWa`cbeffff__afff_ggggWWBBBBBBBUXW\\YZcffbef_fbcZZa^^
28
+ EOT
29
+ expect(@fs.to_s).to eq(result)
30
+ end
31
+ end
@@ -0,0 +1,81 @@
1
+ require 'spec_helper'
2
+ describe MgNu::Sequence do
3
+ before do
4
+ @s = MgNu::Sequence.new(:type => 'dna', :sequence => 'atgcatgcatgcatgcaaaa')
5
+ end
6
+
7
+ it 'knows about attributes' do
8
+ expect(@s).to be_a(MgNu::Sequence)
9
+ expect(@s).to respond_to(:value)
10
+ expect(@s).to respond_to(:value=)
11
+ expect(@s).to respond_to(:sequence)
12
+ expect(@s).to respond_to(:sequence=)
13
+ expect(@s).to respond_to(:type)
14
+ expect(@s).to respond_to(:reverse_complement)
15
+ expect(@s).to respond_to(:translate)
16
+ expect(@s).to respond_to(:levenshtein_distance)
17
+ expect(@s).to respond_to(:distance)
18
+ expect(@s).to respond_to(:percent_identity)
19
+ expect(@s).to respond_to(:identity)
20
+ end
21
+
22
+ it 'can determine dna/rna/protein' do
23
+ expect(@s.dna?).to be(true)
24
+ expect(@s.rna?).to be(false)
25
+ expect(@s.aa?).to be(false)
26
+ expect(@s.aminoacid?).to be(false)
27
+ expect(@s.protein?).to be(false)
28
+ end
29
+
30
+ it 'can reverse complement' do
31
+ expect(@s.reverse_complement).to eq('ttttgcatgcatgcatgcat')
32
+ end
33
+
34
+ it 'sequence unchanged after reverse complement' do
35
+ @s.reverse_complement
36
+ expect(@s.sequence).to eq('atgcatgcatgcatgcaaaa')
37
+ end
38
+
39
+ it 'sequence changed after reverse complement!' do
40
+ @s.reverse_complement!
41
+ expect(@s.sequence).to eq('ttttgcatgcatgcatgcat')
42
+ end
43
+
44
+ it 'can be changed' do
45
+ @s.value = 'atgc'
46
+ expect(@s.value).to eq('atgc')
47
+ @s.sequence = 'tacg'
48
+ expect(@s.sequence).to eq('tacg')
49
+ end
50
+
51
+ it 'can be translated' do
52
+ expect(@s.translate).to eq('MHACMQ')
53
+ expect(@s.translate(1)).to eq('MHACMQ')
54
+ expect(@s.translate(2)).to eq('CMHACK')
55
+ expect(@s.translate(3)).to eq('ACMHAK')
56
+ expect(@s.translate(-1)).to eq('FCMHAC')
57
+ end
58
+
59
+ it 'can compute a levenshtein distance' do
60
+ @s.sequence = 'kitten'
61
+ other = MgNu::Sequence.new(:value => 'knitting')
62
+ expect(@s.distance('knitting')).to eq(3)
63
+ expect(@s.distance(other)).to eq(3)
64
+ end
65
+
66
+ it 'can determine percent identity' do
67
+ @s.sequence = 'acgt'
68
+ other = MgNu::Sequence.new(:value => 'acgg')
69
+ expect(@s.identity('acgt')).to eq(1.0)
70
+ expect(@s.identity('acgg')).to eq(0.75)
71
+ expect(@s.identity(other)).to eq(0.75)
72
+ end
73
+
74
+ it 'can find blocks of N characters' do
75
+ sequence_with_nblocks = MgNu::Sequence.new(:type => 'dna',
76
+ :sequence => 'atgnnnncatgnnnnnnnncatgcnnnnnnnatgcnnnnaaaa')
77
+ pieces = sequence_with_nblocks.nblocks(3)
78
+ expect(pieces.length).to eq(5)
79
+ expect(pieces).to eq([1..3, 8..11, 20..24, 32..35, 40..43])
80
+ end
81
+ end
@@ -0,0 +1,7 @@
1
+ require 'spec_helper'
2
+
3
+ describe MgNu do
4
+ it 'has a version number' do
5
+ expect(MgNu::Version).not_to be nil
6
+ end
7
+ end
@@ -0,0 +1,53 @@
1
+ $LOAD_PATH.unshift File.expand_path('../../lib', __FILE__)
2
+ require 'rspec'
3
+ require 'timecop'
4
+
5
+ require 'mgnu'
6
+
7
+ # set up configure for RSpec
8
+ RSpec.configure do |config|
9
+ # config.before { MgNu::XXXXXX.reset_configuration }
10
+ config.expect_with :rspec do |c|
11
+ c.syntax = :expect
12
+ end
13
+ end
14
+
15
+ # base fixture path
16
+ #
17
+ # @return [String] load path for fixtures
18
+ def fixture_path
19
+ File.expand_path('../fixtures', __FILE__)
20
+ end
21
+
22
+ # return json given a fixture file name
23
+ #
24
+ # @param [String] file name
25
+ # @return [Hash] json hash
26
+ def fixture(file)
27
+ File.read(fixture_path + '/' + file)
28
+ end
29
+
30
+ # return multiple fixtures given multiple file names
31
+ #
32
+ # @param [Array] file names
33
+ # @return [Array] array of json hashes
34
+ def fixtures(files)
35
+ all = []
36
+ files.each do |file|
37
+ all << Yajl::Parser.parse(File.read(fixture_path + '/' + file))
38
+ end
39
+ Yajl::Encoder.encode(all)
40
+ end
41
+
42
+ # return a group of fixtures repeated count times
43
+ #
44
+ # @param [String,Fixnum] file name and integer count
45
+ # @return [Array] array of json hashes
46
+ def fixture_set(file, count)
47
+ all = []
48
+ content = Yajl::Parser.parse(fixture(file))
49
+ (1 .. count).each do
50
+ all << content
51
+ end
52
+ Yajl::Encoder.encode(all)
53
+ end
metadata ADDED
@@ -0,0 +1,376 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: mgnu
3
+ version: !ruby/object:Gem::Version
4
+ version: 2.1.1
5
+ platform: ruby
6
+ authors:
7
+ - Brian C. Thomas
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2018-10-18 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: naught
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - "~>"
18
+ - !ruby/object:Gem::Version
19
+ version: '0.0'
20
+ - - ">="
21
+ - !ruby/object:Gem::Version
22
+ version: 0.0.1
23
+ type: :runtime
24
+ prerelease: false
25
+ version_requirements: !ruby/object:Gem::Requirement
26
+ requirements:
27
+ - - "~>"
28
+ - !ruby/object:Gem::Version
29
+ version: '0.0'
30
+ - - ">="
31
+ - !ruby/object:Gem::Version
32
+ version: 0.0.1
33
+ - !ruby/object:Gem::Dependency
34
+ name: moneta
35
+ requirement: !ruby/object:Gem::Requirement
36
+ requirements:
37
+ - - "~>"
38
+ - !ruby/object:Gem::Version
39
+ version: '0.0'
40
+ - - ">="
41
+ - !ruby/object:Gem::Version
42
+ version: 0.0.1
43
+ type: :runtime
44
+ prerelease: false
45
+ version_requirements: !ruby/object:Gem::Requirement
46
+ requirements:
47
+ - - "~>"
48
+ - !ruby/object:Gem::Version
49
+ version: '0.0'
50
+ - - ">="
51
+ - !ruby/object:Gem::Version
52
+ version: 0.0.1
53
+ - !ruby/object:Gem::Dependency
54
+ name: tokyocabinet
55
+ requirement: !ruby/object:Gem::Requirement
56
+ requirements:
57
+ - - "~>"
58
+ - !ruby/object:Gem::Version
59
+ version: '1.29'
60
+ - - ">="
61
+ - !ruby/object:Gem::Version
62
+ version: 1.29.1
63
+ type: :runtime
64
+ prerelease: false
65
+ version_requirements: !ruby/object:Gem::Requirement
66
+ requirements:
67
+ - - "~>"
68
+ - !ruby/object:Gem::Version
69
+ version: '1.29'
70
+ - - ">="
71
+ - !ruby/object:Gem::Version
72
+ version: 1.29.1
73
+ - !ruby/object:Gem::Dependency
74
+ name: ox
75
+ requirement: !ruby/object:Gem::Requirement
76
+ requirements:
77
+ - - "~>"
78
+ - !ruby/object:Gem::Version
79
+ version: '2.8'
80
+ - - ">="
81
+ - !ruby/object:Gem::Version
82
+ version: 2.8.2
83
+ type: :runtime
84
+ prerelease: false
85
+ version_requirements: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - "~>"
88
+ - !ruby/object:Gem::Version
89
+ version: '2.8'
90
+ - - ">="
91
+ - !ruby/object:Gem::Version
92
+ version: 2.8.2
93
+ - !ruby/object:Gem::Dependency
94
+ name: memoizable
95
+ requirement: !ruby/object:Gem::Requirement
96
+ requirements:
97
+ - - "~>"
98
+ - !ruby/object:Gem::Version
99
+ version: '0.0'
100
+ - - ">="
101
+ - !ruby/object:Gem::Version
102
+ version: 0.0.1
103
+ type: :runtime
104
+ prerelease: false
105
+ version_requirements: !ruby/object:Gem::Requirement
106
+ requirements:
107
+ - - "~>"
108
+ - !ruby/object:Gem::Version
109
+ version: '0.0'
110
+ - - ">="
111
+ - !ruby/object:Gem::Version
112
+ version: 0.0.1
113
+ - !ruby/object:Gem::Dependency
114
+ name: yard
115
+ requirement: !ruby/object:Gem::Requirement
116
+ requirements:
117
+ - - "~>"
118
+ - !ruby/object:Gem::Version
119
+ version: '0.9'
120
+ - - ">="
121
+ - !ruby/object:Gem::Version
122
+ version: 0.9.11
123
+ type: :runtime
124
+ prerelease: false
125
+ version_requirements: !ruby/object:Gem::Requirement
126
+ requirements:
127
+ - - "~>"
128
+ - !ruby/object:Gem::Version
129
+ version: '0.9'
130
+ - - ">="
131
+ - !ruby/object:Gem::Version
132
+ version: 0.9.11
133
+ - !ruby/object:Gem::Dependency
134
+ name: rake
135
+ requirement: !ruby/object:Gem::Requirement
136
+ requirements:
137
+ - - "~>"
138
+ - !ruby/object:Gem::Version
139
+ version: '12.0'
140
+ - - ">="
141
+ - !ruby/object:Gem::Version
142
+ version: 12.0.0
143
+ type: :runtime
144
+ prerelease: false
145
+ version_requirements: !ruby/object:Gem::Requirement
146
+ requirements:
147
+ - - "~>"
148
+ - !ruby/object:Gem::Version
149
+ version: '12.0'
150
+ - - ">="
151
+ - !ruby/object:Gem::Version
152
+ version: 12.0.0
153
+ - !ruby/object:Gem::Dependency
154
+ name: mime-types
155
+ requirement: !ruby/object:Gem::Requirement
156
+ requirements:
157
+ - - "~>"
158
+ - !ruby/object:Gem::Version
159
+ version: '0.0'
160
+ - - ">"
161
+ - !ruby/object:Gem::Version
162
+ version: 0.0.1
163
+ type: :development
164
+ prerelease: false
165
+ version_requirements: !ruby/object:Gem::Requirement
166
+ requirements:
167
+ - - "~>"
168
+ - !ruby/object:Gem::Version
169
+ version: '0.0'
170
+ - - ">"
171
+ - !ruby/object:Gem::Version
172
+ version: 0.0.1
173
+ - !ruby/object:Gem::Dependency
174
+ name: rspec
175
+ requirement: !ruby/object:Gem::Requirement
176
+ requirements:
177
+ - - "~>"
178
+ - !ruby/object:Gem::Version
179
+ version: '0.0'
180
+ - - ">"
181
+ - !ruby/object:Gem::Version
182
+ version: 0.0.1
183
+ type: :development
184
+ prerelease: false
185
+ version_requirements: !ruby/object:Gem::Requirement
186
+ requirements:
187
+ - - "~>"
188
+ - !ruby/object:Gem::Version
189
+ version: '0.0'
190
+ - - ">"
191
+ - !ruby/object:Gem::Version
192
+ version: 0.0.1
193
+ - !ruby/object:Gem::Dependency
194
+ name: rubocop
195
+ requirement: !ruby/object:Gem::Requirement
196
+ requirements:
197
+ - - "~>"
198
+ - !ruby/object:Gem::Version
199
+ version: '0.49'
200
+ - - ">="
201
+ - !ruby/object:Gem::Version
202
+ version: 0.49.0
203
+ type: :development
204
+ prerelease: false
205
+ version_requirements: !ruby/object:Gem::Requirement
206
+ requirements:
207
+ - - "~>"
208
+ - !ruby/object:Gem::Version
209
+ version: '0.49'
210
+ - - ">="
211
+ - !ruby/object:Gem::Version
212
+ version: 0.49.0
213
+ - !ruby/object:Gem::Dependency
214
+ name: timecop
215
+ requirement: !ruby/object:Gem::Requirement
216
+ requirements:
217
+ - - "~>"
218
+ - !ruby/object:Gem::Version
219
+ version: '0.0'
220
+ - - ">"
221
+ - !ruby/object:Gem::Version
222
+ version: 0.0.1
223
+ type: :development
224
+ prerelease: false
225
+ version_requirements: !ruby/object:Gem::Requirement
226
+ requirements:
227
+ - - "~>"
228
+ - !ruby/object:Gem::Version
229
+ version: '0.0'
230
+ - - ">"
231
+ - !ruby/object:Gem::Version
232
+ version: 0.0.1
233
+ - !ruby/object:Gem::Dependency
234
+ name: yardstick
235
+ requirement: !ruby/object:Gem::Requirement
236
+ requirements:
237
+ - - "~>"
238
+ - !ruby/object:Gem::Version
239
+ version: '0.0'
240
+ - - ">"
241
+ - !ruby/object:Gem::Version
242
+ version: 0.0.1
243
+ type: :development
244
+ prerelease: false
245
+ version_requirements: !ruby/object:Gem::Requirement
246
+ requirements:
247
+ - - "~>"
248
+ - !ruby/object:Gem::Version
249
+ version: '0.0'
250
+ - - ">"
251
+ - !ruby/object:Gem::Version
252
+ version: 0.0.1
253
+ - !ruby/object:Gem::Dependency
254
+ name: simplecov
255
+ requirement: !ruby/object:Gem::Requirement
256
+ requirements:
257
+ - - "~>"
258
+ - !ruby/object:Gem::Version
259
+ version: '0.0'
260
+ - - ">"
261
+ - !ruby/object:Gem::Version
262
+ version: 0.0.1
263
+ type: :development
264
+ prerelease: false
265
+ version_requirements: !ruby/object:Gem::Requirement
266
+ requirements:
267
+ - - "~>"
268
+ - !ruby/object:Gem::Version
269
+ version: '0.0'
270
+ - - ">"
271
+ - !ruby/object:Gem::Version
272
+ version: 0.0.1
273
+ description: Lightweight ruby bioinformatics library
274
+ email:
275
+ - bct.x42@gmail.com
276
+ executables: []
277
+ extensions: []
278
+ extra_rdoc_files: []
279
+ files:
280
+ - ".yardopts"
281
+ - README.md
282
+ - Rakefile
283
+ - lib/mgnu.rb
284
+ - lib/mgnu/alignment.rb
285
+ - lib/mgnu/common.rb
286
+ - lib/mgnu/genbank.rb
287
+ - lib/mgnu/genbank/feature.rb
288
+ - lib/mgnu/genbank/location.rb
289
+ - lib/mgnu/genbank/qualifier.rb
290
+ - lib/mgnu/genbank/reference.rb
291
+ - lib/mgnu/genbank/source.rb
292
+ - lib/mgnu/loggable.rb
293
+ - lib/mgnu/parser.rb
294
+ - lib/mgnu/parser/blast.rb
295
+ - lib/mgnu/parser/blast/format0.rb
296
+ - lib/mgnu/parser/blast/format7.rb
297
+ - lib/mgnu/parser/blast/format8.rb
298
+ - lib/mgnu/parser/blast/hsp.rb
299
+ - lib/mgnu/parser/blast/query.rb
300
+ - lib/mgnu/parser/blast/sbjct.rb
301
+ - lib/mgnu/parser/clustalw.rb
302
+ - lib/mgnu/parser/fasta.rb
303
+ - lib/mgnu/parser/fasta_header_index.rb
304
+ - lib/mgnu/parser/fasta_index.rb
305
+ - lib/mgnu/parser/fastq.rb
306
+ - lib/mgnu/parser/genbank.rb
307
+ - lib/mgnu/parser/gff.rb
308
+ - lib/mgnu/parser/iprscan/hit.rb
309
+ - lib/mgnu/parser/iprscan_file.rb
310
+ - lib/mgnu/parser/kegg_ontology_index.rb
311
+ - lib/mgnu/parser/pilercr.rb
312
+ - lib/mgnu/parser/prodigal.rb
313
+ - lib/mgnu/parser/sam.rb
314
+ - lib/mgnu/parser/sam/alignment.rb
315
+ - lib/mgnu/parser/sam/header.rb
316
+ - lib/mgnu/parser/sam/pair.rb
317
+ - lib/mgnu/sequence.rb
318
+ - lib/mgnu/sequence/fasta.rb
319
+ - lib/mgnu/sequence/fastq.rb
320
+ - lib/mgnu/version.rb
321
+ - mgnu.gemspec
322
+ - spec/mgnu/parser/blast_format0_spec.rb
323
+ - spec/mgnu/parser/blast_format7_spec.rb
324
+ - spec/mgnu/parser/blast_format8_spec.rb
325
+ - spec/mgnu/parser/blast_multihsp_spec.rb
326
+ - spec/mgnu/parser/blast_oof_spec.rb
327
+ - spec/mgnu/parser/clustalw_spec.rb
328
+ - spec/mgnu/parser/fasta_header_index_tc_parser_spec.rb
329
+ - spec/mgnu/parser/fasta_index_tc_parser_spec.rb
330
+ - spec/mgnu/parser/fasta_parser_spec.rb
331
+ - spec/mgnu/parser_spec.rb
332
+ - spec/mgnu/sequence/fasta_spec.rb
333
+ - spec/mgnu/sequence/fastq_spec.rb
334
+ - spec/mgnu/sequence_spec.rb
335
+ - spec/mgnu_spec.rb
336
+ - spec/spec_helper.rb
337
+ homepage: http://www.metagenomi.co
338
+ licenses:
339
+ - MIT
340
+ metadata: {}
341
+ post_install_message:
342
+ rdoc_options: []
343
+ require_paths:
344
+ - lib
345
+ required_ruby_version: !ruby/object:Gem::Requirement
346
+ requirements:
347
+ - - ">="
348
+ - !ruby/object:Gem::Version
349
+ version: '0'
350
+ required_rubygems_version: !ruby/object:Gem::Requirement
351
+ requirements:
352
+ - - ">="
353
+ - !ruby/object:Gem::Version
354
+ version: '0'
355
+ requirements: []
356
+ rubyforge_project:
357
+ rubygems_version: 2.7.6
358
+ signing_key:
359
+ specification_version: 4
360
+ summary: MgNu Ruby Bioinformatics Library
361
+ test_files:
362
+ - spec/mgnu/parser/blast_format0_spec.rb
363
+ - spec/mgnu/parser/blast_format7_spec.rb
364
+ - spec/mgnu/parser/blast_format8_spec.rb
365
+ - spec/mgnu/parser/blast_multihsp_spec.rb
366
+ - spec/mgnu/parser/blast_oof_spec.rb
367
+ - spec/mgnu/parser/clustalw_spec.rb
368
+ - spec/mgnu/parser/fasta_header_index_tc_parser_spec.rb
369
+ - spec/mgnu/parser/fasta_index_tc_parser_spec.rb
370
+ - spec/mgnu/parser/fasta_parser_spec.rb
371
+ - spec/mgnu/parser_spec.rb
372
+ - spec/mgnu/sequence/fasta_spec.rb
373
+ - spec/mgnu/sequence/fastq_spec.rb
374
+ - spec/mgnu/sequence_spec.rb
375
+ - spec/mgnu_spec.rb
376
+ - spec/spec_helper.rb