basil 0.0.4 → 0.1.1

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.
data/Gemfile CHANGED
@@ -1,7 +1,13 @@
1
1
  source :rubygems
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  gemspec
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+
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  gem "dna"
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- gem "awesome_print"
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  gem "trollop"
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- gem "rspec"
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- gem "awesome_print"
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+
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+ group :development do
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+ gem 'jeweler'
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+ end
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+
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+ group :test do
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+ gem 'rspec'
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+ end
data/Rakefile CHANGED
@@ -1 +1,48 @@
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- require "bundler/gem_tasks"
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+ # encoding: utf-8
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+
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+ require 'rubygems'
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+ require 'bundler'
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+
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+ require './lib/basil/version.rb'
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+
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'rake'
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+
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ gem.name = "basil"
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+ gem.homepage = "http://audy.github.com/basil"
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+ gem.license = "MIT"
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+ gem.summary = "Weapons-grade HTML demultiplexer"
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+ gem.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
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+ gem.email = "harekrishna@gmail.com"
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+ gem.authors = ["Austin G. Davis-Richardson"]
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+ gem.version = Basil::Version::STRING
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+ end
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+ Jeweler::RubygemsDotOrgTasks.new
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+
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+ require 'rake/testtask'
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+ Rake::TestTask.new(:test) do |test|
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+ test.libs << 'lib' << 'test'
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+ test.pattern = 'test/**/test_*.rb'
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+ test.verbose = true
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+ end
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+
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+ task :default => :test
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+
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+ require 'rdoc/task'
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+ Rake::RDocTask.new do |rdoc|
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+
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+ version = Basil::Version::STRING
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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "test #{version}"
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+ rdoc.rdoc_files.include('readme.md')
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+ rdoc.rdoc_files.include('lib/**/*.rb')
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+ end
@@ -1,22 +1,78 @@
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+ # Generated by jeweler
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+ # DO NOT EDIT THIS FILE DIRECTLY
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+ # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- $:.push File.expand_path("../lib", __FILE__)
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- require 'basil/version'
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  Gem::Specification.new do |s|
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- s.name = 'basil'
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- s.version = '0.0.4'
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- s.authors = ["Austin G. Davis-Richardson"]
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- s.email = ["harekrishna@gmail.com"]
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- s.homepage = "http://github.com/audy/basil"
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- s.summary = 'HTPS demultiplexer'
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- s.description = 'Split multiplexed high-throughput sequencing reads by barcode.'
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- s.rubyforge_project = "basil"
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- s.files = `git ls-files`.split("\n")
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- s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n")
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- s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
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+ s.name = "basil"
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+ s.version = "0.1.1"
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+
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+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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+ s.authors = ["Austin G. Davis-Richardson"]
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+ s.date = "2012-09-18"
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+ s.description = "Split multiplexed Illumina/454/IonTorrent/etc... output by barcode"
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+ s.email = "harekrishna@gmail.com"
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+ s.executables = ["basil"]
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+ s.files = [
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+ ".rspec",
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+ ".rvmrc",
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+ "Gemfile",
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+ "Rakefile",
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+ "basil.gemspec",
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+ "bin/basil",
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+ "lib/basil.rb",
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+ "lib/basil/barcodes.rb",
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+ "lib/basil/basil.rb",
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+ "lib/basil/buffer.rb",
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+ "lib/basil/cli.rb",
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+ "lib/basil/version.rb",
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+ "readme.md",
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+ "spec/basil_spec.rb",
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+ "spec/buffer_spec.rb",
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+ "spec/cli_spec.rb",
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+ "spec/data/barcodes.csv",
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+ "spec/data/illumina/s_1_1_001_qseq.txt",
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+ "spec/data/illumina/s_1_2_001_qseq.txt",
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+ "spec/data/illumina/s_1_3_001_qseq.txt",
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+ "spec/data/test.fasta",
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+ "spec/data/test.fastq",
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+ "spec/data/test.qseq",
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+ "spec/spec_helper.rb"
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+ ]
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+ s.homepage = "http://audy.github.com/basil"
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+ s.licenses = ["MIT"]
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  s.require_paths = ["lib"]
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- s.add_dependency('dna')
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- s.add_dependency('trollop')
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- s.add_dependency('rspec')
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- s.add_dependency('bundler')
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+ s.rubygems_version = "1.8.24"
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+ s.summary = "Weapons-grade HTML demultiplexer"
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+
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+ if s.respond_to? :specification_version then
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+ s.specification_version = 3
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+
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+ if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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+ s.add_runtime_dependency(%q<basil>, [">= 0"])
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+ s.add_runtime_dependency(%q<dna>, [">= 0"])
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+ s.add_runtime_dependency(%q<trollop>, [">= 0"])
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+ s.add_development_dependency(%q<jeweler>, [">= 0"])
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+ s.add_development_dependency(%q<jeweler>, [">= 0"])
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+ s.add_development_dependency(%q<jeweler>, [">= 0"])
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+ s.add_development_dependency(%q<jeweler>, [">= 0"])
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+ else
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+ s.add_dependency(%q<basil>, [">= 0"])
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+ s.add_dependency(%q<dna>, [">= 0"])
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+ s.add_dependency(%q<trollop>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ end
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+ else
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+ s.add_dependency(%q<basil>, [">= 0"])
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+ s.add_dependency(%q<dna>, [">= 0"])
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+ s.add_dependency(%q<trollop>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ s.add_dependency(%q<jeweler>, [">= 0"])
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+ end
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  end
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+
@@ -0,0 +1,9 @@
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+ module Basil
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+ module Version
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+ MAJOR = 0
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+ MINOR = 1
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+ PATCH = 1
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+
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+ STRING = [MAJOR, MINOR, PATCH].join('.')
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+ end
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+ end
@@ -19,6 +19,10 @@ describe Basil::Basil do
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  barcodes.should_not raise_error TypeError
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  end
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+ it 'has a version number' do
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+ Basil::Version::STRING.should_not be_nil
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+ end
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+
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  it 'raises an error if duplicate barcodes are specified' do
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  Basil::Basil.new({ 1 => 'gggg', 2 => 'gggg' }).should raise_error
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  end
@@ -32,16 +36,16 @@ describe Basil::Basil do
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  basil.recognize("NGATC").first.should == 1
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  end
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- it 'preserves case sensitivity of regexp' do
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+ it '#recognize preserves case sensitivity when given regexp' do
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  basil = Basil::Basil.new(1 => /^.GATC/)
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  basil.recognize("Ngatc").should be_nil
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  end
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- it '#recognize is case insensitive' do
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+ it '#recognize is case sensitive' do
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  basil.recognize(dna.upcase!).first.should == 1
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  end
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- it '#recognize ^ is prepended to barcode regexp if strings are provided' do
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+ it '#recognize ^ is automatically prepended to barcode regexp if strings are provided' do
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  basil.recognize('aggggaaa').should be_nil
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  end
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@@ -1,3 +1,5 @@
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  $LOAD_PATH << File.join(File.dirname(__FILE__), 'lib')
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- require 'basil'
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+ require 'basil'
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+
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+ Bundler.require :test
metadata CHANGED
@@ -1,13 +1,13 @@
1
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  --- !ruby/object:Gem::Specification
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  name: basil
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  version: !ruby/object:Gem::Version
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- hash: 23
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+ hash: 25
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  prerelease:
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  segments:
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  - 0
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- - 0
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- - 4
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- version: 0.0.4
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+ - 1
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+ - 1
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+ version: 0.1.1
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  platform: ruby
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  authors:
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  - Austin G. Davis-Richardson
@@ -15,11 +15,10 @@ autorequire:
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  bindir: bin
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16
  cert_chain: []
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17
 
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- date: 2012-05-15 00:00:00 Z
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+ date: 2012-09-18 00:00:00 Z
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19
  dependencies:
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20
  - !ruby/object:Gem::Dependency
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- name: dna
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- prerelease: false
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+ type: :runtime
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  requirement: &id001 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
@@ -29,11 +28,11 @@ dependencies:
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  segments:
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  - 0
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  version: "0"
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- type: :runtime
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  version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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- name: trollop
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+ name: basil
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33
  prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ type: :runtime
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  requirement: &id002 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
@@ -43,11 +42,11 @@ dependencies:
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  segments:
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43
  - 0
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  version: "0"
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- type: :runtime
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  version_requirements: *id002
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- - !ruby/object:Gem::Dependency
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- name: rspec
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+ name: dna
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47
  prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ type: :runtime
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50
  requirement: &id003 !ruby/object:Gem::Requirement
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51
  none: false
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  requirements:
@@ -57,11 +56,11 @@ dependencies:
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  segments:
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  - 0
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  version: "0"
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- type: :runtime
61
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  version_requirements: *id003
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- - !ruby/object:Gem::Dependency
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- name: bundler
60
+ name: trollop
64
61
  prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ type: :development
65
64
  requirement: &id004 !ruby/object:Gem::Requirement
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65
  none: false
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66
  requirements:
@@ -71,11 +70,53 @@ dependencies:
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  segments:
72
71
  - 0
73
72
  version: "0"
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- type: :runtime
75
73
  version_requirements: *id004
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- description: Split multiplexed high-throughput sequencing reads by barcode.
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- email:
78
- - harekrishna@gmail.com
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+ name: jeweler
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+ prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ type: :development
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+ requirement: &id005 !ruby/object:Gem::Requirement
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+ none: false
80
+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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+ version_requirements: *id005
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+ name: jeweler
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+ prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ type: :development
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+ requirement: &id006 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
100
+ version: "0"
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+ version_requirements: *id006
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+ name: jeweler
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+ prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ type: :development
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+ requirement: &id007 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ 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/audy/basil
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: basil
179
+ rubyforge_project:
139
180
  rubygems_version: 1.8.24
140
181
  signing_key:
141
182
  specification_version: 3
142
- summary: HTPS demultiplexer
143
- test_files:
144
- - spec/basil_spec.rb
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
@@ -1,2 +0,0 @@
1
- Gemfile.lock
2
- pkg/