basil 0.0.1
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- data/bin/basil +29 -0
- data/lib/basil.rb +3 -0
- data/readme.md +11 -0
- data/spec/basil_spec.rb +38 -0
- data/spec/buffer_spec.rb +15 -0
- data/spec/spec_helper.rb +3 -0
- metadata +84 -0
data/bin/basil
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#!/usr/bin/env ruby
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require 'ostruct'
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require 'optparse'
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require 'pp'
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require 'bundler'
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Bundler.require :default
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opts = Trollop::options do
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version "Basil PRE-RELEASE"
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banner <<-EOS
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Basil is an HTPS demultiplexer
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Usage:
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basil [options] -i <reads/directory> -o <output directory>
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where [options] are:
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EOS
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opt :barcodes, 'barcodes definition file', short: 'b', type: String
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opt :reads, 'reads (fastq/fasta/qseq)', short: 'i'
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opt :illumina, 'Illumina output directory', short: 'd'
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opt :pretrim, 'trim N nucleotides from start', type: Integer
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opt :afttrim, 'trim N nucleotides from end', type: Integer
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opt :out, 'output directory', short: 'o', type: String
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end
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filename = ARGV.shift
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data/lib/basil.rb
ADDED
data/readme.md
ADDED
data/spec/basil_spec.rb
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require 'spec_helper'
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describe Basil do
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let (:barcodes) {
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{
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1 => 'gggg',
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2 => 'aaaa',
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3 => 'tttt',
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4 => 'cccc',
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}
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}
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let (:basil) { Basil.new barcodes }
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let (:dna) { 'ggggtcatcatcatcatcatcatca' }
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it 'can be created' do
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barcodes.should_not raise_error TypeError
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end
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it 'raises an error if duplicate barcodes are specified' do
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Basil.new({ 1 => 'gggg', 2 => 'gggg' }).should raise_error
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end
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it '#recognize returns the name of matched barcode' do
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basil.recognize(dna).should == 1
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end
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it '#recognize is case insensitive' do
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basil.recognize(dna.upcase!).should == 1
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end
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it '#recognize does not recognize barcodes in the middle of sequences' do
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basil.recognize('aggggaaa').should be_nil
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end
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end
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data/spec/buffer_spec.rb
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require 'spec_helper'
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describe Buffer do
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let (:buffer) { Buffer.new }
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it 'can be created' do
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buffer.should_not raise_error TypeError
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end
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it 'can be given stuff' do
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buffer['thing'] << 'another thing'
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buffer['thing'].first.should == 'another thing'
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end
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end
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data/spec/spec_helper.rb
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metadata
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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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version: 0.0.1
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prerelease:
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platform: ruby
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authors:
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- Austin G. Davis-Richardson
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2010-02-10 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: dna
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requirement: &70286137539700 !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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version: 0.0.0
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type: :runtime
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prerelease: false
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version_requirements: *70286137539700
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- !ruby/object:Gem::Dependency
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name: trollop
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requirement: &70286137539140 !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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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *70286137539140
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: &70286137538460 !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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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *70286137538460
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description: Split multiplexed high-throughput sequencing reads by barcode.
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email: harekrishna@gmail.com
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executables:
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- basil
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extensions: []
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extra_rdoc_files: []
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files:
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- lib/basil.rb
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- spec/basil_spec.rb
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- spec/buffer_spec.rb
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- spec/spec_helper.rb
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- readme.md
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- bin/basil
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homepage: http://github.com/audy/basil
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licenses: []
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !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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version: '0'
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required_rubygems_version: !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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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 1.8.15
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signing_key:
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specification_version: 3
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summary: HTPS demultiplexer
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test_files: []
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