bio-gggenome 0.1.0
Sign up to get free protection for your applications and to get access to all the features.
- data/.document +5 -0
- data/.travis.yml +12 -0
- data/Gemfile +14 -0
- data/LICENSE.txt +20 -0
- data/README.md +57 -0
- data/README.rdoc +48 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/lib/bio-gggenome.rb +12 -0
- data/lib/bio-gggenome/gggenome.rb +85 -0
- data/test/helper.rb +17 -0
- data/test/test_bio-gggenome.rb +84 -0
- metadata +143 -0
data/.document
ADDED
data/.travis.yml
ADDED
@@ -0,0 +1,12 @@
|
|
1
|
+
language: ruby
|
2
|
+
rvm:
|
3
|
+
- 1.9.2
|
4
|
+
- 1.9.3
|
5
|
+
- jruby-19mode # JRuby in 1.9 mode
|
6
|
+
- rbx-19mode
|
7
|
+
# - 1.8.7
|
8
|
+
# - jruby-18mode # JRuby in 1.8 mode
|
9
|
+
# - rbx-18mode
|
10
|
+
|
11
|
+
# uncomment this line if your project needs to run something other than `rake`:
|
12
|
+
# script: bundle exec rspec spec
|
data/Gemfile
ADDED
@@ -0,0 +1,14 @@
|
|
1
|
+
source "http://rubygems.org"
|
2
|
+
# Add dependencies required to use your gem here.
|
3
|
+
# Example:
|
4
|
+
# gem "activesupport", ">= 2.3.5"
|
5
|
+
|
6
|
+
# Add dependencies to develop your gem here.
|
7
|
+
# Include everything needed to run rake, tests, features, etc.
|
8
|
+
group :development do
|
9
|
+
gem "rdoc", "~> 3.12"
|
10
|
+
gem "bundler", ">= 1.0.0"
|
11
|
+
gem "jeweler", "~> 1.8.4"
|
12
|
+
gem "bio", ">= 1.4.2"
|
13
|
+
gem "rdoc", "~> 3.12"
|
14
|
+
end
|
data/LICENSE.txt
ADDED
@@ -0,0 +1,20 @@
|
|
1
|
+
Copyright (c) 2013 Mitsuteru Nakao
|
2
|
+
|
3
|
+
Permission is hereby granted, free of charge, to any person obtaining
|
4
|
+
a copy of this software and associated documentation files (the
|
5
|
+
"Software"), to deal in the Software without restriction, including
|
6
|
+
without limitation the rights to use, copy, modify, merge, publish,
|
7
|
+
distribute, sublicense, and/or sell copies of the Software, and to
|
8
|
+
permit persons to whom the Software is furnished to do so, subject to
|
9
|
+
the following conditions:
|
10
|
+
|
11
|
+
The above copyright notice and this permission notice shall be
|
12
|
+
included in all copies or substantial portions of the Software.
|
13
|
+
|
14
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
15
|
+
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
16
|
+
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
17
|
+
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
|
18
|
+
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
|
19
|
+
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
|
20
|
+
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
data/README.md
ADDED
@@ -0,0 +1,57 @@
|
|
1
|
+
# bio-gggenome
|
2
|
+
|
3
|
+
[![Build Status](https://secure.travis-ci.org/nakao/bioruby-gggenome.png)](http://travis-ci.org/nakao/bioruby-gggenome)
|
4
|
+
|
5
|
+
Ruby client for GGGenome the Ultrafast sequence search, http://gggenome.dbcls.jp/en/
|
6
|
+
|
7
|
+
Note: this software is under active development!
|
8
|
+
|
9
|
+
## Installation
|
10
|
+
|
11
|
+
```sh
|
12
|
+
gem install bio-gggenome
|
13
|
+
```
|
14
|
+
|
15
|
+
## Usage
|
16
|
+
|
17
|
+
```ruby
|
18
|
+
require 'bio-gggenome'
|
19
|
+
db = "hg19"
|
20
|
+
missmatch = 1
|
21
|
+
query = "TTCATTGACAACATT"
|
22
|
+
hits = Bio::GGGenome.search(db, missmatch, query)
|
23
|
+
|
24
|
+
hits['results'].each do |hit|
|
25
|
+
hit['name'] #=> 'chr1'
|
26
|
+
hit['position'] #=> 83462476
|
27
|
+
hit['strand'] #=> "+"
|
28
|
+
end
|
29
|
+
```
|
30
|
+
|
31
|
+
The API doc is online. For more code examples see the test files in
|
32
|
+
the source tree.
|
33
|
+
|
34
|
+
## Project home page
|
35
|
+
|
36
|
+
Information on the source tree, documentation, examples, issues and
|
37
|
+
how to contribute, see
|
38
|
+
|
39
|
+
http://github.com/nakao/bio-gggenome
|
40
|
+
|
41
|
+
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
|
42
|
+
|
43
|
+
## Cite
|
44
|
+
|
45
|
+
If you use this software, please cite one of
|
46
|
+
|
47
|
+
* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
|
48
|
+
* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
|
49
|
+
|
50
|
+
## Biogems.info
|
51
|
+
|
52
|
+
This Biogem is published at [#bio-gggenome](http://biogems.info/index.html)
|
53
|
+
|
54
|
+
## Copyright
|
55
|
+
|
56
|
+
Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.
|
57
|
+
|
data/README.rdoc
ADDED
@@ -0,0 +1,48 @@
|
|
1
|
+
= bio-gggenome
|
2
|
+
|
3
|
+
{<img
|
4
|
+
src="https://secure.travis-ci.org/nakao/bioruby-gggenome.png"
|
5
|
+
/>}[http://travis-ci.org/#!/nakao/bioruby-gggenome]
|
6
|
+
|
7
|
+
Full description goes here
|
8
|
+
|
9
|
+
Note: this software is under active development!
|
10
|
+
|
11
|
+
== Installation
|
12
|
+
|
13
|
+
gem install bio-gggenome
|
14
|
+
|
15
|
+
== Usage
|
16
|
+
|
17
|
+
== Developers
|
18
|
+
|
19
|
+
To use the library
|
20
|
+
|
21
|
+
require 'bio-gggenome'
|
22
|
+
|
23
|
+
The API doc is online. For more code examples see also the test files in
|
24
|
+
the source tree.
|
25
|
+
|
26
|
+
== Project home page
|
27
|
+
|
28
|
+
Information on the source tree, documentation, issues and how to contribute, see
|
29
|
+
|
30
|
+
http://github.com/nakao/bioruby-gggenome
|
31
|
+
|
32
|
+
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
|
33
|
+
|
34
|
+
== Cite
|
35
|
+
|
36
|
+
If you use this software, please cite one of
|
37
|
+
|
38
|
+
* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
|
39
|
+
* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
|
40
|
+
|
41
|
+
== Biogems.info
|
42
|
+
|
43
|
+
This Biogem is published at http://biogems.info/index.html#bio-gggenome
|
44
|
+
|
45
|
+
== Copyright
|
46
|
+
|
47
|
+
Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.
|
48
|
+
|
data/Rakefile
ADDED
@@ -0,0 +1,45 @@
|
|
1
|
+
# encoding: utf-8
|
2
|
+
|
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
|
+
require 'rake'
|
13
|
+
|
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-gggenome"
|
18
|
+
gem.homepage = "http://github.com/nakao/bio-gggenome"
|
19
|
+
gem.license = "MIT"
|
20
|
+
gem.summary = %Q{GGGenome ruby client}
|
21
|
+
gem.description = %Q{A Ruby client for GGGenome the Ultrafast sequence search}
|
22
|
+
gem.email = "mitsuteru.nakao@gmail.com"
|
23
|
+
gem.authors = ["Mitsuteru Nakao"]
|
24
|
+
# dependencies defined in Gemfile
|
25
|
+
end
|
26
|
+
Jeweler::RubygemsDotOrgTasks.new
|
27
|
+
|
28
|
+
require 'rake/testtask'
|
29
|
+
Rake::TestTask.new(:test) do |test|
|
30
|
+
test.libs << 'lib' << 'test'
|
31
|
+
test.pattern = 'test/**/test_*.rb'
|
32
|
+
test.verbose = true
|
33
|
+
end
|
34
|
+
|
35
|
+
task :default => :test
|
36
|
+
|
37
|
+
require 'rdoc/task'
|
38
|
+
Rake::RDocTask.new do |rdoc|
|
39
|
+
version = File.exist?('VERSION') ? File.read('VERSION') : ""
|
40
|
+
|
41
|
+
rdoc.rdoc_dir = 'rdoc'
|
42
|
+
rdoc.title = "bio-gggenome #{version}"
|
43
|
+
rdoc.rdoc_files.include('README*')
|
44
|
+
rdoc.rdoc_files.include('lib/**/*.rb')
|
45
|
+
end
|
data/VERSION
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
0.1.0
|
data/lib/bio-gggenome.rb
ADDED
@@ -0,0 +1,12 @@
|
|
1
|
+
# Please require your code below, respecting the naming conventions in the
|
2
|
+
# bioruby directory tree.
|
3
|
+
#
|
4
|
+
# For example, say you have a plugin named bio-plugin, the only uncommented
|
5
|
+
# line in this file would be
|
6
|
+
#
|
7
|
+
# require 'bio/bio-plugin/plugin'
|
8
|
+
#
|
9
|
+
# In this file only require other files. Avoid other source code.
|
10
|
+
|
11
|
+
require 'bio-gggenome/gggenome.rb'
|
12
|
+
|
@@ -0,0 +1,85 @@
|
|
1
|
+
require 'rubygems'
|
2
|
+
require 'json'
|
3
|
+
require 'uri'
|
4
|
+
require 'bio'
|
5
|
+
|
6
|
+
module Bio
|
7
|
+
|
8
|
+
# Bio::GGGenome
|
9
|
+
#
|
10
|
+
# gggenome = Bio::GGGenome.new
|
11
|
+
# hits = gggenome.search("hg19", 1, "TTCATTGACAACATT")
|
12
|
+
# hits = gggenome.search("hg19", "TTCATTGACAACATT")
|
13
|
+
# hits = gggenome.search("TTCATTGACAACATT")
|
14
|
+
#
|
15
|
+
# hits = Bio::GGGenome.search("hg19", "TTCATTGACAACATT")
|
16
|
+
#
|
17
|
+
class GGGenome
|
18
|
+
BASE_URL = "http://gggenome.dbcls.jp"
|
19
|
+
|
20
|
+
def self.search(*args)
|
21
|
+
new.search(args)
|
22
|
+
end
|
23
|
+
|
24
|
+
def initialize(uri = BASE_URL)
|
25
|
+
uri = URI.parse(uri) unless uri.kind_of?(URI)
|
26
|
+
@pathbase = uri.path
|
27
|
+
@pathbase = '/' + @pathbase unless /\A\// =~ @pathbase
|
28
|
+
@pathbase = @pathbase + '/' unless /\/\z/ =~ @pathbase
|
29
|
+
@http = Bio::Command.new_http(uri.host, uri.port)
|
30
|
+
@header = {
|
31
|
+
'User-Agent' => "BioRuby/#{Bio::BIORUBY_VERSION_ID}"
|
32
|
+
}
|
33
|
+
end
|
34
|
+
|
35
|
+
# Search, returns a result hash.
|
36
|
+
# Bio::GGGenome#search("hg19", 1, "TTCATTGACAACATT")
|
37
|
+
# Bio::GGGenome#search("hg19", "TTCATTGACAACATT")
|
38
|
+
# Bio::GGGenome#search(1, "TTCATTGACAACATT")
|
39
|
+
# Bio::GGGenome#search("TTCATTGACAACATT")
|
40
|
+
# Bio::GGGenome#search("http://gggenome.dbcls.jp/hg19/TTCATTGACAACATTGCGT.json")
|
41
|
+
def search(*args)
|
42
|
+
db = nil
|
43
|
+
missmatch = nil
|
44
|
+
|
45
|
+
if args[0] =~ /^http/
|
46
|
+
args[0].sub!(BASE_URL, '')
|
47
|
+
args[0].sub!(/^\//,'')
|
48
|
+
args[0].sub!(".json", '')
|
49
|
+
args = args[0].split("/")
|
50
|
+
end
|
51
|
+
|
52
|
+
case args.size
|
53
|
+
when 1
|
54
|
+
seq = args.shift
|
55
|
+
when 2
|
56
|
+
if args[0].to_s.strip =~ /^[0-9]+$/
|
57
|
+
missmatch,seq = args
|
58
|
+
else
|
59
|
+
db,seq = args
|
60
|
+
end
|
61
|
+
when 3
|
62
|
+
db,missmatch,seq = args
|
63
|
+
else
|
64
|
+
raise ArgumentError
|
65
|
+
end
|
66
|
+
query = ['', db, missmatch, seq].compact.join("/")
|
67
|
+
path = query + ".json"
|
68
|
+
begin
|
69
|
+
response = @http.get(path, @header)
|
70
|
+
rescue
|
71
|
+
end
|
72
|
+
|
73
|
+
case response.code
|
74
|
+
when "200"
|
75
|
+
JSON.parse(response.body)
|
76
|
+
when "302"
|
77
|
+
location = response.header['Location']
|
78
|
+
search(location)
|
79
|
+
else
|
80
|
+
nil
|
81
|
+
end
|
82
|
+
end
|
83
|
+
end
|
84
|
+
|
85
|
+
end
|
data/test/helper.rb
ADDED
@@ -0,0 +1,17 @@
|
|
1
|
+
require 'rubygems'
|
2
|
+
require 'bundler'
|
3
|
+
begin
|
4
|
+
Bundler.setup(:default, :development)
|
5
|
+
rescue Bundler::BundlerError => e
|
6
|
+
$stderr.puts e.message
|
7
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
8
|
+
exit e.status_code
|
9
|
+
end
|
10
|
+
require 'test/unit'
|
11
|
+
|
12
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
13
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
14
|
+
require 'bio-gggenome'
|
15
|
+
|
16
|
+
class Test::Unit::TestCase
|
17
|
+
end
|
@@ -0,0 +1,84 @@
|
|
1
|
+
require 'helper'
|
2
|
+
|
3
|
+
class TestBioGggenome < Test::Unit::TestCase
|
4
|
+
|
5
|
+
def test_new
|
6
|
+
assert(Bio::GGGenome.new)
|
7
|
+
end
|
8
|
+
|
9
|
+
def test_search_result_is_a_hash
|
10
|
+
g = Bio::GGGenome.new
|
11
|
+
hits = g.search('hg19', '1', 'TTCATTGACAACATT')
|
12
|
+
assert_equal(Hash, hits.class)
|
13
|
+
end
|
14
|
+
|
15
|
+
def test_search_arguments_3_and_2
|
16
|
+
g = Bio::GGGenome.new
|
17
|
+
hits = g.search('hg19', '0', 'TTCATTGACAACATT')
|
18
|
+
hits1 = g.search('hg19', 'TTCATTGACAACATT')
|
19
|
+
assert_equal(hits['summary'][0]['count'], hits1['summary'][0]['count'])
|
20
|
+
assert_equal(hits['summary'][1]['count'], hits1['summary'][1]['count'])
|
21
|
+
assert_equal(hits['summary'][0]['count_is_approx'], hits1['summary'][0]['count_is_approx'])
|
22
|
+
assert_equal(hits['summary'][0]['query'], hits1['summary'][0]['query'])
|
23
|
+
end
|
24
|
+
|
25
|
+
def test_class_method_search
|
26
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
27
|
+
assert_equal(Hash, hits.class)
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_hits_hash_keys
|
31
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
32
|
+
assert_equal(['database', 'error', 'results', 'summary', 'time'].sort,
|
33
|
+
hits.keys.sort)
|
34
|
+
end
|
35
|
+
|
36
|
+
def test_hits_database
|
37
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
38
|
+
assert_equal("Human genome, GRCh37/hg19 (Feb, 2009)", hits["database"])
|
39
|
+
end
|
40
|
+
|
41
|
+
def test_hits_error
|
42
|
+
hits = Bio::GGGenome.search('hg19', '1', 'TTCATTGACAACATT')
|
43
|
+
assert_equal("none", hits["error"])
|
44
|
+
end
|
45
|
+
|
46
|
+
def test_hits_summary
|
47
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
48
|
+
assert_equal(Array, hits["summary"].class)
|
49
|
+
assert_equal(2, hits["summary"].size)
|
50
|
+
assert_equal(['count', 'count_is_approx', 'query'].sort, hits["summary"][0].keys.sort)
|
51
|
+
assert_equal(15, hits["summary"][0]['count'])
|
52
|
+
assert_equal(false, hits["summary"][0]['count_is_approx'])
|
53
|
+
assert_equal('TTCATTGACAACATT', hits["summary"][0]['query'])
|
54
|
+
end
|
55
|
+
|
56
|
+
def test_hits_time
|
57
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
58
|
+
assert_equal(Date.today, Date.parse(hits["time"]))
|
59
|
+
end
|
60
|
+
|
61
|
+
def test_hits_results_size
|
62
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
63
|
+
assert_equal(23, hits["results"].size)
|
64
|
+
end
|
65
|
+
|
66
|
+
def test_hits_results_keys
|
67
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
68
|
+
assert_equal(['name', 'position', 'position_end', 'snippet', 'snippet_pos', 'snippet_end', 'strand'].sort,
|
69
|
+
hits["results"][0].keys.sort)
|
70
|
+
end
|
71
|
+
|
72
|
+
def test_hits_results_0
|
73
|
+
hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
|
74
|
+
assert_equal("chr1", hits["results"][0]['name'])
|
75
|
+
assert_equal(83462476, hits["results"][0]['position'])
|
76
|
+
assert_equal(83462490, hits["results"][0]['position_end'])
|
77
|
+
assert_equal("TTCTCTTCCTCCTCCTCCTCAGCCTCAACATGAAGATGATGAAAATGGAGACCTTCATCGTGATCCACTTCTAATTAATGAATAGTAAGTATATTTTCTCTTCATTGACAACATTTTTCCTCTTACTTTATTGTAAGAATACAATATACGATATATATTGCCATGCAAAATATGTGTTAATTGACTATATTATATTATTGATAGGACTTCTTGAG",
|
78
|
+
hits["results"][0]['snippet'])
|
79
|
+
assert_equal(83462376, hits["results"][0]['snippet_pos'])
|
80
|
+
assert_equal(83462590, hits["results"][0]['snippet_end'])
|
81
|
+
assert_equal("+", hits["results"][0]['strand'])
|
82
|
+
end
|
83
|
+
|
84
|
+
end
|
metadata
ADDED
@@ -0,0 +1,143 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-gggenome
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.0
|
5
|
+
prerelease:
|
6
|
+
platform: ruby
|
7
|
+
authors:
|
8
|
+
- Mitsuteru Nakao
|
9
|
+
autorequire:
|
10
|
+
bindir: bin
|
11
|
+
cert_chain: []
|
12
|
+
date: 2013-08-12 00:00:00.000000000 Z
|
13
|
+
dependencies:
|
14
|
+
- !ruby/object:Gem::Dependency
|
15
|
+
name: rdoc
|
16
|
+
requirement: !ruby/object:Gem::Requirement
|
17
|
+
none: false
|
18
|
+
requirements:
|
19
|
+
- - ~>
|
20
|
+
- !ruby/object:Gem::Version
|
21
|
+
version: '3.12'
|
22
|
+
type: :development
|
23
|
+
prerelease: false
|
24
|
+
version_requirements: !ruby/object:Gem::Requirement
|
25
|
+
none: false
|
26
|
+
requirements:
|
27
|
+
- - ~>
|
28
|
+
- !ruby/object:Gem::Version
|
29
|
+
version: '3.12'
|
30
|
+
- !ruby/object:Gem::Dependency
|
31
|
+
name: bundler
|
32
|
+
requirement: !ruby/object:Gem::Requirement
|
33
|
+
none: false
|
34
|
+
requirements:
|
35
|
+
- - ! '>='
|
36
|
+
- !ruby/object:Gem::Version
|
37
|
+
version: 1.0.0
|
38
|
+
type: :development
|
39
|
+
prerelease: false
|
40
|
+
version_requirements: !ruby/object:Gem::Requirement
|
41
|
+
none: false
|
42
|
+
requirements:
|
43
|
+
- - ! '>='
|
44
|
+
- !ruby/object:Gem::Version
|
45
|
+
version: 1.0.0
|
46
|
+
- !ruby/object:Gem::Dependency
|
47
|
+
name: jeweler
|
48
|
+
requirement: !ruby/object:Gem::Requirement
|
49
|
+
none: false
|
50
|
+
requirements:
|
51
|
+
- - ~>
|
52
|
+
- !ruby/object:Gem::Version
|
53
|
+
version: 1.8.4
|
54
|
+
type: :development
|
55
|
+
prerelease: false
|
56
|
+
version_requirements: !ruby/object:Gem::Requirement
|
57
|
+
none: false
|
58
|
+
requirements:
|
59
|
+
- - ~>
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: 1.8.4
|
62
|
+
- !ruby/object:Gem::Dependency
|
63
|
+
name: bio
|
64
|
+
requirement: !ruby/object:Gem::Requirement
|
65
|
+
none: false
|
66
|
+
requirements:
|
67
|
+
- - ! '>='
|
68
|
+
- !ruby/object:Gem::Version
|
69
|
+
version: 1.4.2
|
70
|
+
type: :development
|
71
|
+
prerelease: false
|
72
|
+
version_requirements: !ruby/object:Gem::Requirement
|
73
|
+
none: false
|
74
|
+
requirements:
|
75
|
+
- - ! '>='
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: 1.4.2
|
78
|
+
- !ruby/object:Gem::Dependency
|
79
|
+
name: rdoc
|
80
|
+
requirement: !ruby/object:Gem::Requirement
|
81
|
+
none: false
|
82
|
+
requirements:
|
83
|
+
- - ~>
|
84
|
+
- !ruby/object:Gem::Version
|
85
|
+
version: '3.12'
|
86
|
+
type: :development
|
87
|
+
prerelease: false
|
88
|
+
version_requirements: !ruby/object:Gem::Requirement
|
89
|
+
none: false
|
90
|
+
requirements:
|
91
|
+
- - ~>
|
92
|
+
- !ruby/object:Gem::Version
|
93
|
+
version: '3.12'
|
94
|
+
description: A Ruby client for GGGenome the Ultrafast sequence search
|
95
|
+
email: mitsuteru.nakao@gmail.com
|
96
|
+
executables: []
|
97
|
+
extensions: []
|
98
|
+
extra_rdoc_files:
|
99
|
+
- LICENSE.txt
|
100
|
+
- README.md
|
101
|
+
- README.rdoc
|
102
|
+
files:
|
103
|
+
- .document
|
104
|
+
- .travis.yml
|
105
|
+
- Gemfile
|
106
|
+
- LICENSE.txt
|
107
|
+
- README.md
|
108
|
+
- README.rdoc
|
109
|
+
- Rakefile
|
110
|
+
- VERSION
|
111
|
+
- lib/bio-gggenome.rb
|
112
|
+
- lib/bio-gggenome/gggenome.rb
|
113
|
+
- test/helper.rb
|
114
|
+
- test/test_bio-gggenome.rb
|
115
|
+
homepage: http://github.com/nakao/bio-gggenome
|
116
|
+
licenses:
|
117
|
+
- MIT
|
118
|
+
post_install_message:
|
119
|
+
rdoc_options: []
|
120
|
+
require_paths:
|
121
|
+
- lib
|
122
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
123
|
+
none: false
|
124
|
+
requirements:
|
125
|
+
- - ! '>='
|
126
|
+
- !ruby/object:Gem::Version
|
127
|
+
version: '0'
|
128
|
+
segments:
|
129
|
+
- 0
|
130
|
+
hash: 1277551901848741236
|
131
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
132
|
+
none: false
|
133
|
+
requirements:
|
134
|
+
- - ! '>='
|
135
|
+
- !ruby/object:Gem::Version
|
136
|
+
version: '0'
|
137
|
+
requirements: []
|
138
|
+
rubyforge_project:
|
139
|
+
rubygems_version: 1.8.23
|
140
|
+
signing_key:
|
141
|
+
specification_version: 3
|
142
|
+
summary: GGGenome ruby client
|
143
|
+
test_files: []
|