basil 0.0.4 → 0.1.1
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- data/Gemfile +9 -3
- data/Rakefile +48 -1
- data/basil.gemspec +73 -17
- data/lib/basil/version.rb +9 -0
- data/spec/basil_spec.rb +7 -3
- data/spec/spec_helper.rb +3 -1
- metadata +69 -38
- data/.gitignore +0 -2
data/Gemfile
CHANGED
data/Rakefile
CHANGED
@@ -1 +1,48 @@
|
|
1
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-
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1
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+
# encoding: utf-8
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2
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+
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3
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+
require 'rubygems'
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4
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+
require 'bundler'
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5
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+
|
6
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+
require './lib/basil/version.rb'
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7
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+
|
8
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+
begin
|
9
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+
Bundler.setup(:default, :development)
|
10
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+
rescue Bundler::BundlerError => e
|
11
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+
$stderr.puts e.message
|
12
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+
$stderr.puts "Run `bundle install` to install missing gems"
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13
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+
exit e.status_code
|
14
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+
end
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15
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+
require 'rake'
|
16
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+
|
17
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+
require 'jeweler'
|
18
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+
Jeweler::Tasks.new do |gem|
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19
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+
gem.name = "basil"
|
20
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+
gem.homepage = "http://audy.github.com/basil"
|
21
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+
gem.license = "MIT"
|
22
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+
gem.summary = "Weapons-grade HTML demultiplexer"
|
23
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+
gem.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
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24
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+
gem.email = "harekrishna@gmail.com"
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25
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+
gem.authors = ["Austin G. Davis-Richardson"]
|
26
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+
gem.version = Basil::Version::STRING
|
27
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+
end
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28
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+
Jeweler::RubygemsDotOrgTasks.new
|
29
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+
|
30
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+
require 'rake/testtask'
|
31
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+
Rake::TestTask.new(:test) do |test|
|
32
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+
test.libs << 'lib' << 'test'
|
33
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+
test.pattern = 'test/**/test_*.rb'
|
34
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+
test.verbose = true
|
35
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+
end
|
36
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+
|
37
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+
task :default => :test
|
38
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+
|
39
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+
require 'rdoc/task'
|
40
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+
Rake::RDocTask.new do |rdoc|
|
41
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+
|
42
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+
version = Basil::Version::STRING
|
43
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+
|
44
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+
rdoc.rdoc_dir = 'rdoc'
|
45
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+
rdoc.title = "test #{version}"
|
46
|
+
rdoc.rdoc_files.include('readme.md')
|
47
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+
rdoc.rdoc_files.include('lib/**/*.rb')
|
48
|
+
end
|
data/basil.gemspec
CHANGED
@@ -1,22 +1,78 @@
|
|
1
|
+
# Generated by jeweler
|
2
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+
# DO NOT EDIT THIS FILE DIRECTLY
|
3
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+
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
1
4
|
# -*- encoding: utf-8 -*-
|
2
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-
$:.push File.expand_path("../lib", __FILE__)
|
3
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-
require 'basil/version'
|
4
5
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|
5
6
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Gem::Specification.new do |s|
|
6
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-
s.name
|
7
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-
s.version
|
8
|
-
|
9
|
-
s.
|
10
|
-
s.
|
11
|
-
s.
|
12
|
-
s.description =
|
13
|
-
s.
|
14
|
-
s.
|
15
|
-
s.
|
16
|
-
|
7
|
+
s.name = "basil"
|
8
|
+
s.version = "0.1.1"
|
9
|
+
|
10
|
+
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
|
+
s.authors = ["Austin G. Davis-Richardson"]
|
12
|
+
s.date = "2012-09-18"
|
13
|
+
s.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
|
14
|
+
s.email = "harekrishna@gmail.com"
|
15
|
+
s.executables = ["basil"]
|
16
|
+
s.files = [
|
17
|
+
".rspec",
|
18
|
+
".rvmrc",
|
19
|
+
"Gemfile",
|
20
|
+
"Rakefile",
|
21
|
+
"basil.gemspec",
|
22
|
+
"bin/basil",
|
23
|
+
"lib/basil.rb",
|
24
|
+
"lib/basil/barcodes.rb",
|
25
|
+
"lib/basil/basil.rb",
|
26
|
+
"lib/basil/buffer.rb",
|
27
|
+
"lib/basil/cli.rb",
|
28
|
+
"lib/basil/version.rb",
|
29
|
+
"readme.md",
|
30
|
+
"spec/basil_spec.rb",
|
31
|
+
"spec/buffer_spec.rb",
|
32
|
+
"spec/cli_spec.rb",
|
33
|
+
"spec/data/barcodes.csv",
|
34
|
+
"spec/data/illumina/s_1_1_001_qseq.txt",
|
35
|
+
"spec/data/illumina/s_1_2_001_qseq.txt",
|
36
|
+
"spec/data/illumina/s_1_3_001_qseq.txt",
|
37
|
+
"spec/data/test.fasta",
|
38
|
+
"spec/data/test.fastq",
|
39
|
+
"spec/data/test.qseq",
|
40
|
+
"spec/spec_helper.rb"
|
41
|
+
]
|
42
|
+
s.homepage = "http://audy.github.com/basil"
|
43
|
+
s.licenses = ["MIT"]
|
17
44
|
s.require_paths = ["lib"]
|
18
|
-
s.
|
19
|
-
s.
|
20
|
-
|
21
|
-
s.
|
45
|
+
s.rubygems_version = "1.8.24"
|
46
|
+
s.summary = "Weapons-grade HTML demultiplexer"
|
47
|
+
|
48
|
+
if s.respond_to? :specification_version then
|
49
|
+
s.specification_version = 3
|
50
|
+
|
51
|
+
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
52
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+
s.add_runtime_dependency(%q<basil>, [">= 0"])
|
53
|
+
s.add_runtime_dependency(%q<dna>, [">= 0"])
|
54
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+
s.add_runtime_dependency(%q<trollop>, [">= 0"])
|
55
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+
s.add_development_dependency(%q<jeweler>, [">= 0"])
|
56
|
+
s.add_development_dependency(%q<jeweler>, [">= 0"])
|
57
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+
s.add_development_dependency(%q<jeweler>, [">= 0"])
|
58
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+
s.add_development_dependency(%q<jeweler>, [">= 0"])
|
59
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+
else
|
60
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+
s.add_dependency(%q<basil>, [">= 0"])
|
61
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+
s.add_dependency(%q<dna>, [">= 0"])
|
62
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+
s.add_dependency(%q<trollop>, [">= 0"])
|
63
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
64
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
65
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
66
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
67
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+
end
|
68
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+
else
|
69
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+
s.add_dependency(%q<basil>, [">= 0"])
|
70
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+
s.add_dependency(%q<dna>, [">= 0"])
|
71
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+
s.add_dependency(%q<trollop>, [">= 0"])
|
72
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
73
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
74
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
75
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+
s.add_dependency(%q<jeweler>, [">= 0"])
|
76
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+
end
|
22
77
|
end
|
78
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+
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data/spec/basil_spec.rb
CHANGED
@@ -19,6 +19,10 @@ describe Basil::Basil do
|
|
19
19
|
barcodes.should_not raise_error TypeError
|
20
20
|
end
|
21
21
|
|
22
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+
it 'has a version number' do
|
23
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+
Basil::Version::STRING.should_not be_nil
|
24
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+
end
|
25
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+
|
22
26
|
it 'raises an error if duplicate barcodes are specified' do
|
23
27
|
Basil::Basil.new({ 1 => 'gggg', 2 => 'gggg' }).should raise_error
|
24
28
|
end
|
@@ -32,16 +36,16 @@ describe Basil::Basil do
|
|
32
36
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basil.recognize("NGATC").first.should == 1
|
33
37
|
end
|
34
38
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|
35
|
-
it 'preserves case sensitivity
|
39
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+
it '#recognize preserves case sensitivity when given regexp' do
|
36
40
|
basil = Basil::Basil.new(1 => /^.GATC/)
|
37
41
|
basil.recognize("Ngatc").should be_nil
|
38
42
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end
|
39
43
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|
40
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-
it '#recognize is case
|
44
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+
it '#recognize is case sensitive' do
|
41
45
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basil.recognize(dna.upcase!).first.should == 1
|
42
46
|
end
|
43
47
|
|
44
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-
it '#recognize ^ is prepended to barcode regexp if strings are provided' do
|
48
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+
it '#recognize ^ is automatically prepended to barcode regexp if strings are provided' do
|
45
49
|
basil.recognize('aggggaaa').should be_nil
|
46
50
|
end
|
47
51
|
|
data/spec/spec_helper.rb
CHANGED
metadata
CHANGED
@@ -1,13 +1,13 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: basil
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
hash:
|
4
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+
hash: 25
|
5
5
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prerelease:
|
6
6
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segments:
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7
7
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- 0
|
8
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-
-
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9
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-
-
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10
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-
version: 0.
|
8
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+
- 1
|
9
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+
- 1
|
10
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+
version: 0.1.1
|
11
11
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platform: ruby
|
12
12
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authors:
|
13
13
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- Austin G. Davis-Richardson
|
@@ -15,11 +15,10 @@ autorequire:
|
|
15
15
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bindir: bin
|
16
16
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cert_chain: []
|
17
17
|
|
18
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-
date: 2012-
|
18
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+
date: 2012-09-18 00:00:00 Z
|
19
19
|
dependencies:
|
20
20
|
- !ruby/object:Gem::Dependency
|
21
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-
|
22
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-
prerelease: false
|
21
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+
type: :runtime
|
23
22
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requirement: &id001 !ruby/object:Gem::Requirement
|
24
23
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none: false
|
25
24
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requirements:
|
@@ -29,11 +28,11 @@ dependencies:
|
|
29
28
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segments:
|
30
29
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- 0
|
31
30
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version: "0"
|
32
|
-
type: :runtime
|
33
31
|
version_requirements: *id001
|
34
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-
|
35
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-
name: trollop
|
32
|
+
name: basil
|
36
33
|
prerelease: false
|
34
|
+
- !ruby/object:Gem::Dependency
|
35
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+
type: :runtime
|
37
36
|
requirement: &id002 !ruby/object:Gem::Requirement
|
38
37
|
none: false
|
39
38
|
requirements:
|
@@ -43,11 +42,11 @@ dependencies:
|
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43
42
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segments:
|
44
43
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- 0
|
45
44
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version: "0"
|
46
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-
type: :runtime
|
47
45
|
version_requirements: *id002
|
48
|
-
|
49
|
-
name: rspec
|
46
|
+
name: dna
|
50
47
|
prerelease: false
|
48
|
+
- !ruby/object:Gem::Dependency
|
49
|
+
type: :runtime
|
51
50
|
requirement: &id003 !ruby/object:Gem::Requirement
|
52
51
|
none: false
|
53
52
|
requirements:
|
@@ -57,11 +56,11 @@ dependencies:
|
|
57
56
|
segments:
|
58
57
|
- 0
|
59
58
|
version: "0"
|
60
|
-
type: :runtime
|
61
59
|
version_requirements: *id003
|
62
|
-
|
63
|
-
name: bundler
|
60
|
+
name: trollop
|
64
61
|
prerelease: false
|
62
|
+
- !ruby/object:Gem::Dependency
|
63
|
+
type: :development
|
65
64
|
requirement: &id004 !ruby/object:Gem::Requirement
|
66
65
|
none: false
|
67
66
|
requirements:
|
@@ -71,11 +70,53 @@ dependencies:
|
|
71
70
|
segments:
|
72
71
|
- 0
|
73
72
|
version: "0"
|
74
|
-
type: :runtime
|
75
73
|
version_requirements: *id004
|
76
|
-
|
77
|
-
|
78
|
-
-
|
74
|
+
name: jeweler
|
75
|
+
prerelease: false
|
76
|
+
- !ruby/object:Gem::Dependency
|
77
|
+
type: :development
|
78
|
+
requirement: &id005 !ruby/object:Gem::Requirement
|
79
|
+
none: false
|
80
|
+
requirements:
|
81
|
+
- - ">="
|
82
|
+
- !ruby/object:Gem::Version
|
83
|
+
hash: 3
|
84
|
+
segments:
|
85
|
+
- 0
|
86
|
+
version: "0"
|
87
|
+
version_requirements: *id005
|
88
|
+
name: jeweler
|
89
|
+
prerelease: false
|
90
|
+
- !ruby/object:Gem::Dependency
|
91
|
+
type: :development
|
92
|
+
requirement: &id006 !ruby/object:Gem::Requirement
|
93
|
+
none: false
|
94
|
+
requirements:
|
95
|
+
- - ">="
|
96
|
+
- !ruby/object:Gem::Version
|
97
|
+
hash: 3
|
98
|
+
segments:
|
99
|
+
- 0
|
100
|
+
version: "0"
|
101
|
+
version_requirements: *id006
|
102
|
+
name: jeweler
|
103
|
+
prerelease: false
|
104
|
+
- !ruby/object:Gem::Dependency
|
105
|
+
type: :development
|
106
|
+
requirement: &id007 !ruby/object:Gem::Requirement
|
107
|
+
none: false
|
108
|
+
requirements:
|
109
|
+
- - ">="
|
110
|
+
- !ruby/object:Gem::Version
|
111
|
+
hash: 3
|
112
|
+
segments:
|
113
|
+
- 0
|
114
|
+
version: "0"
|
115
|
+
version_requirements: *id007
|
116
|
+
name: jeweler
|
117
|
+
prerelease: false
|
118
|
+
description: Split multiplexed Illumina/454/IonTorrent/etc... output by barcode
|
119
|
+
email: harekrishna@gmail.com
|
79
120
|
executables:
|
80
121
|
- basil
|
81
122
|
extensions: []
|
@@ -83,7 +124,6 @@ extensions: []
|
|
83
124
|
extra_rdoc_files: []
|
84
125
|
|
85
126
|
files:
|
86
|
-
- .gitignore
|
87
127
|
- .rspec
|
88
128
|
- .rvmrc
|
89
129
|
- Gemfile
|
@@ -95,6 +135,7 @@ files:
|
|
95
135
|
- lib/basil/basil.rb
|
96
136
|
- lib/basil/buffer.rb
|
97
137
|
- lib/basil/cli.rb
|
138
|
+
- lib/basil/version.rb
|
98
139
|
- readme.md
|
99
140
|
- spec/basil_spec.rb
|
100
141
|
- spec/buffer_spec.rb
|
@@ -107,9 +148,9 @@ files:
|
|
107
148
|
- spec/data/test.fastq
|
108
149
|
- spec/data/test.qseq
|
109
150
|
- spec/spec_helper.rb
|
110
|
-
homepage: http://github.com/
|
111
|
-
licenses:
|
112
|
-
|
151
|
+
homepage: http://audy.github.com/basil
|
152
|
+
licenses:
|
153
|
+
- MIT
|
113
154
|
post_install_message:
|
114
155
|
rdoc_options: []
|
115
156
|
|
@@ -135,20 +176,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
135
176
|
version: "0"
|
136
177
|
requirements: []
|
137
178
|
|
138
|
-
rubyforge_project:
|
179
|
+
rubyforge_project:
|
139
180
|
rubygems_version: 1.8.24
|
140
181
|
signing_key:
|
141
182
|
specification_version: 3
|
142
|
-
summary:
|
143
|
-
test_files:
|
144
|
-
|
145
|
-
- spec/buffer_spec.rb
|
146
|
-
- spec/cli_spec.rb
|
147
|
-
- spec/data/barcodes.csv
|
148
|
-
- spec/data/illumina/s_1_1_001_qseq.txt
|
149
|
-
- spec/data/illumina/s_1_2_001_qseq.txt
|
150
|
-
- spec/data/illumina/s_1_3_001_qseq.txt
|
151
|
-
- spec/data/test.fasta
|
152
|
-
- spec/data/test.fastq
|
153
|
-
- spec/data/test.qseq
|
154
|
-
- spec/spec_helper.rb
|
183
|
+
summary: Weapons-grade HTML demultiplexer
|
184
|
+
test_files: []
|
185
|
+
|
data/.gitignore
DELETED