dna 0.0.1 → 0.0.2

data/lib/dna.rb

@@ -1,10 +1,13 @@
+##
+# Dna
+#
 class Dna # iterator
   include Enumerable
-  
+
   def initialize(handle, args={})
     @handle = handle
-    @format = args[:type].to_sym
-    
+    @format = args[:format].to_sym
+
     @iterator = 
       case @format
       when :fasta
@@ -17,7 +20,7 @@ class Dna # iterator
         raise "#{@type} not supported."
       end
   end
-  
+
   def each &block
     @iterator.each do |r|
       if block_given?
@@ -27,9 +30,9 @@ class Dna # iterator
       end
     end
   end
-  
+
   private
-  
+
   def fasta_parser
     sequence, header = nil, nil
     Enumerator.new do |enum|
@@ -45,27 +48,29 @@ class Dna # iterator
       enum.yield Fasta.new(name: header, sequence: sequence)
     end
   end
-  
+
   def fastq_parser
     c = (0..3).cycle
     Enumerator.new do |enum|
+      params = { name: nil, sequence: nil, quality: nil }
       @handle.each do |line|
         n = c.next
         case n
         when 0
-          header = line.strip
+          params[:name] = line.strip
         when 1
-          sequence = line.strip
+          params[:sequence] = line.strip
         when 2
           nil
         when 3
-          quality = line.strip
-          enum.yield Fastq.new(name: header, sequence: sequence, quality: quality)
+          params[:quality] = line.strip
+          record = Fastq.new params
+          enum.yield record
         end
       end
     end
   end
-  
+
   def qseq_parser
     Enumerator.new do |enum|
       @handle.each do |line|
@@ -100,14 +105,14 @@ end
 #
 class Fasta < Record
   attr_accessor :name, :sequence
-  
+
   def initialize(args={})
     @name = args[:name]
     @sequence = args[:sequence]
   end
-  
+
   def to_s
-    ">#{@name}\n#{@sequence}\n"
+    ">#{@name}\n#{@sequence}"
   end
 end
 
@@ -116,13 +121,13 @@ end
 #
 class Fastq < Record
   attr_accessor :name, :sequence, :format, :quality
-  
+
   def initialize(args={})
     @name = args[:name]
     @sequence = args[:sequence]
     @quality = args[:quality]
   end
-  
+
   def to_s
     "@#{@name}\n#{@sequence}\n+#{@name}\n#{@quality}"
   end
@@ -130,29 +135,23 @@ end
 
 ##
 # QSEQ record
-#
+#2
 class QSEQ < Record
-  attr_accessor :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
-  
+
   def initialize(args={})
-    @machine = args[:machine]
-    @run = args[:run]
-    @lane = args[:lane]
-    @tile = args[:tile]
-    @x = args[:x]
-    @y = args[:y]
-    @index = args[:index]
-    @read_no = args[:read_no]
-    @sequence = args[:sequence]
-    @quality = args[:quality]
-    @filtered = args[:filtered]
+    # These are the properties defined by the qseq spec
+    # they must be in the same order that they appear in the tab-separated qseq file
+    @properties = [:machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered]
+    @properties.each do |p|
+      self.class.send(:define_method, p) { args[p] }
+    end
   end
-  
+
   def to_s
-    [@machine, @run, @lane, @tile, @x, @y, @index, @read_no, @sequence, @quality, @filtered].join("\t")
+    @properties.collect { |x| self.send(x) }.join("\t")
   end
-  
+
   def header
-    [@machine, @run, @lane, @tile, @x, @y, @index, @read_no, @sequence, @quality, @filtered].join(':')
+    @properties.collect { |x| self.send(x) }.join("\t")
   end
 end

data/readme.md

@@ -0,0 +1,47 @@
+# DNA
+
+A minimalistic sequence file parser.
+
+Austin G. Davis-Richardson
+
+Supported Formats:
+
+  - [fasta](http://en.wikipedia.org/wiki/FASTA)
+  - [fastq](http://en.wikipedia.org/wiki/Fastq)
+  - [qseq](http://blog.kokocinski.net/index.php/qseq-files-format?blog=2)
+
+[Request a format](https://github.com/audy/dna/issues/new)
+
+## Installation
+
+With Ruby 1.9.2 or better:
+
+`gem install dna`
+
+## Usage
+
+```ruby
+
+require 'dna'
+
+File.open('sequences.fasta') do |handle|
+  records = Dna.new handle, format: 'fastq'
+  
+  records.each do |record|
+    puts record.length
+  end
+end
+
+File.open('sequences.fastq') do |handle|
+  records = Dna.new handle, format: 'fastq'
+
+  records.each do |record|
+    puts record.quality
+  end
+end
+
+File.open('sequences.qseq') do |handle|
+  records = Dna.new handle, format: 'qseq'
+  puts records.first.inspect
+end
+```

data/spec/dna_spec.rb

@@ -0,0 +1,37 @@
+require 'spec_helper'
+
+describe Dna do
+  include_context "parser stuff"
+
+  let(:fasta) { Dna.new @fasta_file, format: 'fasta' }
+  let (:fastq) { Dna.new @fastq_file, format: 'fastq' }
+  let (:qseq) { Dna.new @qseq_file, format: 'qseq' }
+
+  it 'can parse a crappily formatted fasta file' do
+    fasta.to_a.length.should == 2
+  end
+
+  it 'generates fasta objects from a fasta file' do
+    fasta.first.class.should == Fasta
+  end
+
+  it 'can parse fastq format' do
+    fastq.to_a.length.should == 2
+  end
+
+  it 'generates fastq objects from a fasta file' do
+    fastq.first.class.should == Fastq
+  end
+
+  it 'generates fastq objects from a fasta file' do
+    fastq.first.sequence.should_not be_nil
+  end
+
+  it 'can parse qseq' do
+    qseq.to_a.length.should == 2
+  end
+
+  it 'generates qseq objects from a qseq file' do
+    qseq.first.class.should == QSEQ
+  end
+end

data/spec/record_spec.rb

@@ -0,0 +1,94 @@
+require 'spec_helper'
+
+describe Fasta do
+
+  let (:fasta) { Fasta.new name: 'test', sequence: 'GATC'}
+
+  it 'can be created' do
+    fasta.should_not be_nil
+  end
+
+  it 'has a name' do
+    fasta.name.should_not be_nil
+  end
+
+  it 'has a sequence' do
+    fasta.sequence.should_not be_nil
+  end
+
+  it 'has a length' do
+    fasta.length.should == fasta.sequence.length
+  end
+
+  it 'can be printed as fasta' do
+    fasta.to_s.should == ">#{fasta.name}\n#{fasta.sequence}"
+  end
+end
+
+describe Fastq do
+  let (:fastq) { Fastq.new name: 'test', sequence: 'GATC', quality: 'BBBB' }
+
+  it 'can be created' do
+    fastq.should_not be_nil
+  end
+
+  it 'has a name' do
+    fastq.name.should_not be_nil
+  end
+
+  it 'has a sequence' do
+    fastq.sequence.should_not be_nil
+  end
+
+  it 'has a quality score string' do
+    fastq.quality.should_not be_nil
+  end
+
+  it 'has a length' do
+    fastq.length.should == fastq.sequence.length
+  end
+
+  it 'can be printed as fastq' do
+    fastq.to_s.should == "@#{fastq.name}\n#{fastq.sequence}\n+#{fastq.name}\n#{fastq.quality}"
+  end
+end
+
+describe QSEQ do
+  let (:string) { "HWUSI-EAS1690\t0007\t1\t1\t1139\t20892\t0\t1\tGTGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGTGTAAAGGGCGCGTAGGCGGCCCTGTAAGTCAGTGGTGAAATCTC\tfffffffffffffffeeeeedddddabdd\dddabeeeee^aabdcabddaKdddc`RcY`_c`aT`Ib]Tc^\cZEKOZ_\]\bZVK^UZG]`[^BBBBB\t1" }
+
+  let (:properties) {
+    line = string.split("\t")
+    { machine: line[0],
+      run: line[1],
+      lane: line[2],
+      tile: line[3],
+      x: line[4],
+      y: line[5],
+      index: line[6],
+      read_no: line[7],
+      sequence: line[8],
+      quality: line[9],
+      filtered: line[10] }
+  }
+
+  let (:qseq) {
+    QSEQ.new(properties)}
+
+  it 'can be created' do
+    qseq.should_not be_nil
+  end
+
+  it 'has a header' do
+    qseq.header.should_not be_nil
+  end
+
+  ['machine', 'run', 'lane', 'tile', 'x', 'y', 'index', 'read_no', 'sequence', 'quality', 'filtered'].each do |property|
+    it "has property #{property}" do
+      qseq.send(property).should == properties[property.to_sym]
+    end
+  end
+
+  it 'can be printed back in its original form' do
+    qseq.to_s.should == string
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,17 @@
+$LOAD_PATH << File.join(File.dirname(__FILE__), 'lib')
+
+require 'rspec'
+require 'dna'
+
+path = File.dirname(__FILE__)
+fasta_file = File.readlines(File.join(path, 'data/test.fasta'))
+fastq_file = File.readlines(File.join(path, 'data/test.fastq'))
+qseq_file = File.readlines(File.join(path, 'data/test.qseq'))
+
+shared_context "parser stuff" do
+  before do
+    @fasta_file = fasta_file
+    @fastq_file = fastq_file
+    @qseq_file = qseq_file
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dna
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,15 +9,19 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2010-01-27 00:00:00.000000000 Z
+date: 2010-02-01 00:00:00.000000000 Z
 dependencies: []
-description: for parsing fasta files
+description: for parsing various types of DNA sequence files
 email: harekrishna@gmail.com
 executables: []
 extensions: []
 extra_rdoc_files: []
 files:
 - lib/dna.rb
+- spec/dna_spec.rb
+- spec/record_spec.rb
+- spec/spec_helper.rb
+- readme.md
 homepage: http://github.com/audy/dna
 licenses: []
 post_install_message: 
@@ -41,5 +45,5 @@ rubyforge_project:
 rubygems_version: 1.8.15
 signing_key: 
 specification_version: 3
-summary: fasta parser
+summary: DNA sequence parser
 test_files: []