basil 0.0.1

data/bin/basil

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+#!/usr/bin/env ruby
+
+require 'ostruct'
+require 'optparse'
+require 'pp'
+
+require 'bundler'
+Bundler.require :default
+
+opts = Trollop::options do
+
+  version "Basil PRE-RELEASE"
+  banner <<-EOS
+Basil is an HTPS demultiplexer
+
+Usage:
+    basil [options] -i <reads/directory> -o <output directory>
+where [options] are:
+  EOS
+
+  opt :barcodes, 'barcodes definition file', short: 'b',  type: String
+  opt :reads, 'reads (fastq/fasta/qseq)', short: 'i'
+  opt :illumina, 'Illumina output directory', short: 'd'
+  opt :pretrim, 'trim N nucleotides from start', type: Integer
+  opt :afttrim, 'trim N nucleotides from end', type: Integer
+  opt :out, 'output directory', short: 'o', type: String
+end
+
+filename = ARGV.shift

data/lib/basil.rb

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+Dir.glob(File.join(File.dirname(__FILE__), 'basil', '*.rb')).each do |f|
+  require f
+end

data/readme.md

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+# Basil
+
+Yet another tool for splitting barcoded sequences. It had to be done.
+
+## Installation
+
+    gem install basil
+
+## Usage
+
+    basil -h

data/spec/basil_spec.rb

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+require 'spec_helper'
+
+describe Basil do
+
+  let (:barcodes) {
+    {
+      1 => 'gggg',
+      2 => 'aaaa',
+      3 => 'tttt',
+      4 => 'cccc',
+    }
+  }
+
+  let (:basil) { Basil.new barcodes }
+
+  let (:dna) { 'ggggtcatcatcatcatcatcatca' }
+
+  it 'can be created' do
+    barcodes.should_not raise_error TypeError
+  end
+
+  it 'raises an error if duplicate barcodes are specified' do
+    Basil.new({ 1 => 'gggg', 2 => 'gggg' }).should raise_error
+  end
+
+  it '#recognize returns the name of matched barcode' do
+    basil.recognize(dna).should == 1
+  end
+
+  it '#recognize is case insensitive' do
+    basil.recognize(dna.upcase!).should == 1
+  end
+
+  it '#recognize does not recognize barcodes in the middle of sequences' do
+    basil.recognize('aggggaaa').should be_nil
+  end
+  
+end

data/spec/buffer_spec.rb

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+require 'spec_helper'
+
+describe Buffer do
+
+  let (:buffer) { Buffer.new }
+
+  it 'can be created' do
+    buffer.should_not raise_error TypeError
+  end
+
+  it 'can be given stuff' do
+    buffer['thing'] << 'another thing'
+    buffer['thing'].first.should == 'another thing'
+  end
+end

data/spec/spec_helper.rb

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+$LOAD_PATH << File.join(File.dirname(__FILE__), 'lib')
+
+require 'basil'

metadata

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+--- !ruby/object:Gem::Specification
+name: basil
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Austin G. Davis-Richardson
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2010-02-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: dna
+  requirement: &70286137539700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70286137539700
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: &70286137539140 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70286137539140
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &70286137538460 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70286137538460
+description: Split multiplexed high-throughput sequencing reads by barcode.
+email: harekrishna@gmail.com
+executables:
+- basil
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/basil.rb
+- spec/basil_spec.rb
+- spec/buffer_spec.rb
+- spec/spec_helper.rb
+- readme.md
+- bin/basil
+homepage: http://github.com/audy/basil
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.15
+signing_key: 
+specification_version: 3
+summary: HTPS demultiplexer
+test_files: []