bio-velvet 0.0.1

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Files changed (28) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.rspec +1 -0
  4. data/.travis.yml +12 -0
  5. data/Gemfile +17 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +62 -0
  8. data/Rakefile +49 -0
  9. data/VERSION +1 -0
  10. data/lib/bio-velvet.rb +13 -0
  11. data/lib/bio-velvet/graph.rb +517 -0
  12. data/lib/bio-velvet/runner.rb +91 -0
  13. data/spec/bio-velvet_arc_array_spec.rb +123 -0
  14. data/spec/bio-velvet_graph_spec.rb +290 -0
  15. data/spec/bio-velvet_runner_spec.rb +67 -0
  16. data/spec/data/node_sequence/LastGraph +33 -0
  17. data/spec/data/node_sequence/contigs.fa +75 -0
  18. data/spec/data/runner_input.fa +18 -0
  19. data/spec/data/short_node_LastGraph +40 -0
  20. data/spec/data/short_node_sequence_test_graph +20 -0
  21. data/spec/data/velvet_test_reads_assembly/Graph +3465 -0
  22. data/spec/data/velvet_test_reads_assembly/HOWTO_RECREATE +2 -0
  23. data/spec/data/velvet_test_reads_assembly/LastGraph +3462 -0
  24. data/spec/data/velvet_test_reads_assembly_read_tracking/Graph2 +45602 -0
  25. data/spec/data/velvet_test_reads_assembly_read_tracking/HOWTO_RECREATE +2 -0
  26. data/spec/data/velvet_test_trail_sequence_assembly/reads1.fa +18 -0
  27. data/spec/spec_helper.rb +14 -0
  28. metadata +211 -0
data/spec/data/velvet_test_reads_assembly_read_tracking/HOWTO_RECREATE ADDED
@@ -0,0 +1,2 @@
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+ $~/bioinfo/velvet/velveth velvet_test_reads_assembly_read_tracking 31 -short -fasta ~/bioinfo/velvet/tests/reads.fa.gz
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+ $~/bioinfo/velvet/velveth velvet_test_reads_assembly_read_tracking -read_trkg
data/spec/data/velvet_test_trail_sequence_assembly/reads1.fa ADDED
@@ -0,0 +1,18 @@
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+ >read1
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+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
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+ TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
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+ ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
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+ CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
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+ GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
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+ CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
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+ ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
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+ GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
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+ ACTATGCTGGTATTTCACTTCCAGGTACAGG
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+ >read2
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+ ACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
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+ CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
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+ ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
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+ GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
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+ ACTATGCTGGTATTTCACTTCCAGGTACAGGTGGAATTGGAACAGATGGATTCATTAAAA
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+ TAGGGCTAGTTTTATTAGGGGTTGTTATTATTCTAGGTGCAGGATATGTTGTCTTAGATA
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+ AAAGAAAGAGAATTTAATTAAATAAAAATATACTTCTTCTATTTTTAT
data/spec/spec_helper.rb ADDED
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ require 'rspec'
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+ require 'bio-velvet'
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+
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+ # Requires supporting files with custom matchers and macros, etc,
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+ # in ./support/ and its subdirectories.
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+ Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
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+
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+ RSpec.configure do |config|
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+
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+ end
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+
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+ TEST_DATA_DIR = File.join(File.dirname(__FILE__),'data')
metadata ADDED
@@ -0,0 +1,211 @@
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+ --- !ruby/object:Gem::Specification
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+ name: bio-velvet
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+ version: !ruby/object:Gem::Version
4
+ version: 0.0.1
5
+ platform: ruby
6
+ authors:
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+ - Ben J Woodcroft
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+ autorequire:
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+ bindir: bin
10
+ cert_chain: []
11
+ date: 2013-12-20 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
14
+ name: bio-logger
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - '>='
18
+ - !ruby/object:Gem::Version
19
+ version: 1.0.1
20
+ type: :runtime
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - '>='
25
+ - !ruby/object:Gem::Version
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+ version: 1.0.1
27
+ - !ruby/object:Gem::Dependency
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+ name: systemu
29
+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
31
+ - - '>='
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+ - !ruby/object:Gem::Version
33
+ version: '0'
34
+ type: :runtime
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+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - '>='
39
+ - !ruby/object:Gem::Version
40
+ version: '0'
41
+ - !ruby/object:Gem::Dependency
42
+ name: files
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
47
+ version: '0'
48
+ type: :runtime
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
54
+ version: '0'
55
+ - !ruby/object:Gem::Dependency
56
+ name: hopcsv
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - '>='
60
+ - !ruby/object:Gem::Version
61
+ version: 0.4.3
62
+ type: :runtime
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+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
66
+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: 0.4.3
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - '>='
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+ - !ruby/object:Gem::Version
75
+ version: 2.8.0
76
+ type: :development
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - '>='
81
+ - !ruby/object:Gem::Version
82
+ version: 2.8.0
83
+ - !ruby/object:Gem::Dependency
84
+ name: rdoc
85
+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - '>='
88
+ - !ruby/object:Gem::Version
89
+ version: '3.12'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - '>='
95
+ - !ruby/object:Gem::Version
96
+ version: '3.12'
97
+ - !ruby/object:Gem::Dependency
98
+ name: jeweler
99
+ requirement: !ruby/object:Gem::Requirement
100
+ requirements:
101
+ - - '>='
102
+ - !ruby/object:Gem::Version
103
+ version: 1.8.4
104
+ type: :development
105
+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - '>='
109
+ - !ruby/object:Gem::Version
110
+ version: 1.8.4
111
+ - !ruby/object:Gem::Dependency
112
+ name: bundler
113
+ requirement: !ruby/object:Gem::Requirement
114
+ requirements:
115
+ - - '>='
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+ - !ruby/object:Gem::Version
117
+ version: 1.0.21
118
+ type: :development
119
+ prerelease: false
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ requirements:
122
+ - - '>='
123
+ - !ruby/object:Gem::Version
124
+ version: 1.0.21
125
+ - !ruby/object:Gem::Dependency
126
+ name: bio
127
+ requirement: !ruby/object:Gem::Requirement
128
+ requirements:
129
+ - - '>='
130
+ - !ruby/object:Gem::Version
131
+ version: 1.4.2
132
+ type: :development
133
+ prerelease: false
134
+ version_requirements: !ruby/object:Gem::Requirement
135
+ requirements:
136
+ - - '>='
137
+ - !ruby/object:Gem::Version
138
+ version: 1.4.2
139
+ - !ruby/object:Gem::Dependency
140
+ name: rdoc
141
+ requirement: !ruby/object:Gem::Requirement
142
+ requirements:
143
+ - - '>='
144
+ - !ruby/object:Gem::Version
145
+ version: '3.12'
146
+ type: :development
147
+ prerelease: false
148
+ version_requirements: !ruby/object:Gem::Requirement
149
+ requirements:
150
+ - - '>='
151
+ - !ruby/object:Gem::Version
152
+ version: '3.12'
153
+ description: Parser to work with some file formats used in the velvet DNA assembler
154
+ email: donttrustben@gmail.com
155
+ executables: []
156
+ extensions: []
157
+ extra_rdoc_files:
158
+ - LICENSE.txt
159
+ - README.md
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+ files:
161
+ - .document
162
+ - .rspec
163
+ - .travis.yml
164
+ - Gemfile
165
+ - LICENSE.txt
166
+ - README.md
167
+ - Rakefile
168
+ - VERSION
169
+ - lib/bio-velvet.rb
170
+ - lib/bio-velvet/graph.rb
171
+ - lib/bio-velvet/runner.rb
172
+ - spec/bio-velvet_arc_array_spec.rb
173
+ - spec/bio-velvet_graph_spec.rb
174
+ - spec/bio-velvet_runner_spec.rb
175
+ - spec/data/node_sequence/LastGraph
176
+ - spec/data/node_sequence/contigs.fa
177
+ - spec/data/runner_input.fa
178
+ - spec/data/short_node_LastGraph
179
+ - spec/data/short_node_sequence_test_graph
180
+ - spec/data/velvet_test_reads_assembly/Graph
181
+ - spec/data/velvet_test_reads_assembly/HOWTO_RECREATE
182
+ - spec/data/velvet_test_reads_assembly/LastGraph
183
+ - spec/data/velvet_test_reads_assembly_read_tracking/Graph2
184
+ - spec/data/velvet_test_reads_assembly_read_tracking/HOWTO_RECREATE
185
+ - spec/data/velvet_test_trail_sequence_assembly/reads1.fa
186
+ - spec/spec_helper.rb
187
+ homepage: http://github.com/wwood/bioruby-velvet
188
+ licenses:
189
+ - MIT
190
+ metadata: {}
191
+ post_install_message:
192
+ rdoc_options: []
193
+ require_paths:
194
+ - lib
195
+ required_ruby_version: !ruby/object:Gem::Requirement
196
+ requirements:
197
+ - - '>='
198
+ - !ruby/object:Gem::Version
199
+ version: '0'
200
+ required_rubygems_version: !ruby/object:Gem::Requirement
201
+ requirements:
202
+ - - '>='
203
+ - !ruby/object:Gem::Version
204
+ version: '0'
205
+ requirements: []
206
+ rubyforge_project:
207
+ rubygems_version: 2.0.3
208
+ signing_key:
209
+ specification_version: 4
210
+ summary: Parser to work with file formats used in the velvet DNA assembler
211
+ test_files: []