bio-locus 0.0.6 → 0.0.7

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@@ -1,8 +1,6 @@
1
1
  language: ruby
2
2
  rvm:
3
- - 1.9.2
4
- - 1.9.3
5
- - jruby-19mode # JRuby in 1.9 mode
3
+ - 2.2.2
6
4
 
7
5
  # - rbx-19mode
8
6
  # - 1.8.7
data/Gemfile CHANGED
@@ -1,14 +1,5 @@
1
1
  source "http://rubygems.org"
2
2
  group :development do
3
- gem "cucumber"
4
- gem "jeweler"
5
- gem "bundler"
3
+ gem "rake"
6
4
  gem "rspec"
7
- gem "tokyocabinet"
8
- gem "localmemcache"
9
- gem "moneta"
10
5
  end
11
- # The following are optional (Ruby serialize is the default)
12
- # gem "tokyocabinet"
13
- # gem "localmemcache"
14
- # gem "moneta"
data/README.md CHANGED
@@ -1,6 +1,6 @@
1
1
  # bio-locus
2
2
 
3
- [![Build Status](https://secure.travis-ci.org/pjotrp/bioruby-locus.png)](http://travis-ci.org/pjotrp/bioruby-locus)
3
+ [![Build Status](https://secure.travis-ci.org/pjotrp/bio-locus.png)](http://travis-ci.org/pjotrp/bio-locus)
4
4
 
5
5
  Bio-locus is a tool for fast querying of genome locations. Many file
6
6
  formats in bioinformatics contain records that start with a chromosome
@@ -16,6 +16,15 @@ Why would you use bio-locus?
16
16
  3. See what positions match an EVS or GoNL database
17
17
  4. Compare locations from databases such as the TCGA and COSMIC
18
18
  5. Comparison of overlap or difference
19
+ 6. Parse and store values to reuse later (nyi)
20
+ 7. Store seek positions (nyi)
21
+
22
+ How does bio-locus differ from tabix? Tabix is a fast indexer for
23
+ tabular data. bio-locus does something similar. The difference is that
24
+ bio-locus is more flexible in matching location data, is line
25
+ based with regex options, can use other back-ends (RAM,
26
+ NoSQL, SQL), and does *not* use bgzip. In other words, bio-locus
27
+ is friendly and more flexible.
19
28
 
20
29
  In principle any of the Moneta supported backends can be used,
21
30
  including LocalMemCache, RubySerialize and TokyoCabinet. The default
@@ -203,7 +212,7 @@ So now we have 99 INDELs for this dataset which are not common INDELs.
203
212
  Information on the source tree, documentation, examples, issues and
204
213
  how to contribute, see
205
214
 
206
- http://github.com/pjotrp/bioruby-locus
215
+ http://github.com/pjotrp/bio-locus
207
216
 
208
217
  The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
209
218
 
data/Rakefile CHANGED
@@ -1,30 +1,8 @@
1
1
  # encoding: utf-8
2
2
 
3
3
  require 'rubygems'
4
- require 'bundler'
5
- begin
6
- Bundler.setup(:default, :development)
7
- rescue Bundler::BundlerError => e
8
- $stderr.puts e.message
9
- $stderr.puts "Run `bundle install` to install missing gems"
10
- exit e.status_code
11
- end
12
4
  require 'rake'
13
5
 
14
- require 'jeweler'
15
- Jeweler::Tasks.new do |gem|
16
- # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
17
- gem.name = "bio-locus"
18
- gem.homepage = "http://github.com/pjotrp/bioruby-locus"
19
- gem.license = "MIT"
20
- gem.summary = %Q{Fast storage and comparison of chr+pos(+alt) locations}
21
- gem.description = %Q{A tool for fast querying and filtering of genome locations in VCF and other formats}
22
- gem.email = "pjotr.public01@thebird.nl"
23
- gem.authors = ["Pjotr Prins"]
24
- # dependencies defined in Gemfile
25
- end
26
- Jeweler::RubygemsDotOrgTasks.new
27
-
28
6
  require 'rspec/core'
29
7
  require 'rspec/core/rake_task'
30
8
  RSpec::Core::RakeTask.new(:spec) do |spec|
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.0.6
1
+ 0.0.7
@@ -12,26 +12,28 @@ describe "BioLocus with Serialize" do
12
12
  File.unlink(fn)
13
13
  end
14
14
 
15
- describe "BioLocus with Moneta" do
16
- fn = 'biolocus_moneta_localmemcache.db'
17
- store = BioLocus::MonetaMapper.new(:LocalMemCache,fn)
18
- store['test'] = 'yes'
19
- store['test2'] = 'no'
20
- a = store['test']
21
- store['test'].should == 'yes'
22
- store['test2'].should == 'no'
23
- store.close
24
- File.unlink(fn)
25
- end
15
+ if false
16
+ describe "BioLocus with Moneta" do
17
+ fn = 'biolocus_moneta_localmemcache.db'
18
+ store = BioLocus::MonetaMapper.new(:LocalMemCache,fn)
19
+ store['test'] = 'yes'
20
+ store['test2'] = 'no'
21
+ a = store['test']
22
+ store['test'].should == 'yes'
23
+ store['test2'].should == 'no'
24
+ store.close
25
+ File.unlink(fn)
26
+ end
26
27
 
27
- describe "BioLocus with TokyoCabinet" do
28
- fn = 'biolocus_tokyocabinet.db'
29
- store = BioLocus::TokyoCabinetMapper.new(fn)
30
- store['test'] = 'yes'
31
- store['test2'] = 'no'
32
- a = store['test']
33
- store['test'].should == 'yes'
34
- store['test2'].should == 'no'
35
- store.close
36
- File.unlink(fn)
28
+ describe "BioLocus with TokyoCabinet" do
29
+ fn = 'biolocus_tokyocabinet.db'
30
+ store = BioLocus::TokyoCabinetMapper.new(fn)
31
+ store['test'] = 'yes'
32
+ store['test2'] = 'no'
33
+ a = store['test']
34
+ store['test'].should == 'yes'
35
+ store['test2'].should == 'no'
36
+ store.close
37
+ File.unlink(fn)
38
+ end
37
39
  end
metadata CHANGED
@@ -1,113 +1,15 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-locus
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.6
4
+ version: 0.0.7
5
5
  platform: ruby
6
6
  authors:
7
7
  - Pjotr Prins
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2014-10-10 00:00:00.000000000 Z
12
- dependencies:
13
- - !ruby/object:Gem::Dependency
14
- name: cucumber
15
- requirement: !ruby/object:Gem::Requirement
16
- requirements:
17
- - - ">="
18
- - !ruby/object:Gem::Version
19
- version: '0'
20
- type: :development
21
- prerelease: false
22
- version_requirements: !ruby/object:Gem::Requirement
23
- requirements:
24
- - - ">="
25
- - !ruby/object:Gem::Version
26
- version: '0'
27
- - !ruby/object:Gem::Dependency
28
- name: jeweler
29
- requirement: !ruby/object:Gem::Requirement
30
- requirements:
31
- - - ">="
32
- - !ruby/object:Gem::Version
33
- version: '0'
34
- type: :development
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: bundler
43
- requirement: !ruby/object:Gem::Requirement
44
- requirements:
45
- - - ">="
46
- - !ruby/object:Gem::Version
47
- version: '0'
48
- type: :development
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: rspec
57
- requirement: !ruby/object:Gem::Requirement
58
- requirements:
59
- - - ">="
60
- - !ruby/object:Gem::Version
61
- version: '0'
62
- type: :development
63
- prerelease: false
64
- version_requirements: !ruby/object:Gem::Requirement
65
- requirements:
66
- - - ">="
67
- - !ruby/object:Gem::Version
68
- version: '0'
69
- - !ruby/object:Gem::Dependency
70
- name: tokyocabinet
71
- requirement: !ruby/object:Gem::Requirement
72
- requirements:
73
- - - ">="
74
- - !ruby/object:Gem::Version
75
- version: '0'
76
- type: :development
77
- prerelease: false
78
- version_requirements: !ruby/object:Gem::Requirement
79
- requirements:
80
- - - ">="
81
- - !ruby/object:Gem::Version
82
- version: '0'
83
- - !ruby/object:Gem::Dependency
84
- name: localmemcache
85
- requirement: !ruby/object:Gem::Requirement
86
- requirements:
87
- - - ">="
88
- - !ruby/object:Gem::Version
89
- version: '0'
90
- type: :development
91
- prerelease: false
92
- version_requirements: !ruby/object:Gem::Requirement
93
- requirements:
94
- - - ">="
95
- - !ruby/object:Gem::Version
96
- version: '0'
97
- - !ruby/object:Gem::Dependency
98
- name: moneta
99
- requirement: !ruby/object:Gem::Requirement
100
- requirements:
101
- - - ">="
102
- - !ruby/object:Gem::Version
103
- version: '0'
104
- type: :development
105
- prerelease: false
106
- version_requirements: !ruby/object:Gem::Requirement
107
- requirements:
108
- - - ">="
109
- - !ruby/object:Gem::Version
110
- version: '0'
11
+ date: 2015-09-14 00:00:00.000000000 Z
12
+ dependencies: []
111
13
  description: A tool for fast querying and filtering of genome locations in VCF and
112
14
  other formats
113
15
  email: pjotr.public01@thebird.nl
@@ -127,9 +29,6 @@ files:
127
29
  - Rakefile
128
30
  - VERSION
129
31
  - bin/bio-locus
130
- - features/bio-locus.feature
131
- - features/step_definitions/bio-locus_steps.rb
132
- - features/support/env.rb
133
32
  - lib/bio-locus.rb
134
33
  - lib/bio-locus/dbmapper.rb
135
34
  - lib/bio-locus/locus.rb
@@ -141,7 +40,7 @@ files:
141
40
  - test/data/input/multisample.vcf
142
41
  - test/data/input/somaticsniper.vcf
143
42
  - test/data/input/test.snv1
144
- homepage: http://github.com/pjotrp/bioruby-locus
43
+ homepage: http://github.com/pjotrp/bio-locus
145
44
  licenses:
146
45
  - MIT
147
46
  metadata: {}
@@ -161,7 +60,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
161
60
  version: '0'
162
61
  requirements: []
163
62
  rubyforge_project:
164
- rubygems_version: 2.0.3
63
+ rubygems_version: 2.4.5.1
165
64
  signing_key:
166
65
  specification_version: 4
167
66
  summary: Fast storage and comparison of chr+pos(+alt) locations
@@ -1,9 +0,0 @@
1
- Feature: something something
2
- In order to something something
3
- A user something something
4
- something something something
5
-
6
- Scenario: something something
7
- Given inspiration
8
- When I create a sweet new gem
9
- Then everyone should see how awesome I am
@@ -1,13 +0,0 @@
1
- require 'bundler'
2
- begin
3
- Bundler.setup(:default, :development)
4
- rescue Bundler::BundlerError => e
5
- $stderr.puts e.message
6
- $stderr.puts "Run `bundle install` to install missing gems"
7
- exit e.status_code
8
- end
9
-
10
- $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
11
- require 'bio-locus'
12
-
13
- require 'rspec/expectations'