bio-velvet 0.0.1

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 (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 @@
1
+ $~/bioinfo/velvet/velveth velvet_test_reads_assembly_read_tracking 31 -short -fasta ~/bioinfo/velvet/tests/reads.fa.gz
2
+ $~/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 @@
1
+ >read1
2
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
3
+ TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
4
+ ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
5
+ CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
6
+ GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
7
+ CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
8
+ ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
9
+ GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
10
+ ACTATGCTGGTATTTCACTTCCAGGTACAGG
11
+ >read2
12
+ ACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
13
+ CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
14
+ ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
15
+ GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
16
+ ACTATGCTGGTATTTCACTTCCAGGTACAGGTGGAATTGGAACAGATGGATTCATTAAAA
17
+ TAGGGCTAGTTTTATTAGGGGTTGTTATTATTCTAGGTGCAGGATATGTTGTCTTAGATA
18
+ AAAGAAAGAGAATTTAATTAAATAAAAATATACTTCTTCTATTTTTAT
data/spec/spec_helper.rb ADDED
@@ -0,0 +1,14 @@
1
+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
2
+ $LOAD_PATH.unshift(File.dirname(__FILE__))
3
+ require 'rspec'
4
+ require 'bio-velvet'
5
+
6
+ # Requires supporting files with custom matchers and macros, etc,
7
+ # in ./support/ and its subdirectories.
8
+ Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
9
+
10
+ RSpec.configure do |config|
11
+
12
+ end
13
+
14
+ TEST_DATA_DIR = File.join(File.dirname(__FILE__),'data')
metadata ADDED
@@ -0,0 +1,211 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: bio-velvet
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.1
5
+ platform: ruby
6
+ authors:
7
+ - Ben J Woodcroft
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2013-12-20 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !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
26
+ version: 1.0.1
27
+ - !ruby/object:Gem::Dependency
28
+ name: systemu
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - '>='
32
+ - !ruby/object:Gem::Version
33
+ version: '0'
34
+ type: :runtime
35
+ 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:
45
+ - - '>='
46
+ - !ruby/object:Gem::Version
47
+ version: '0'
48
+ type: :runtime
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - '>='
53
+ - !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
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - '>='
67
+ - !ruby/object:Gem::Version
68
+ version: 0.4.3
69
+ - !ruby/object:Gem::Dependency
70
+ name: rspec
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - '>='
74
+ - !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
+ - - '>='
116
+ - !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
160
+ 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: []