dna 0.0.5 → 0.0.6

data/lib/dna.rb

@@ -1,22 +1,24 @@
+Dir.glob(File.join(File.dirname(__FILE__), 'parsers', '*.rb')).each { |f| require f }
+
 ##
 # Dna
 #
-class Dna # iterator
+class Dna
   include Enumerable
 
   attr_reader :format
 
-  def initialize(handle, args={})
+  def initialize(handle)
     @handle = handle
     @format = detect_format
     @iterator =
       case @format
       when :fasta
-        fasta_parser
+        FastaParser.new @handle
       when :fastq
-        fastq_parser
+        FastqParser.new @handle
       when :qseq
-        qseq_parser
+        QSEQParser.new @handle
       else
         raise "#{@format} not supported."
       end
@@ -39,75 +41,7 @@ class Dna # iterator
   end
 
   def each &block
-    @iterator.each do |r|
-      if block_given?
-        block.call r
-      else
-        yield r
-      end
-    end
-  end
-
-  private
-
-  def fasta_parser
-    sequence, header = nil, nil
-    Enumerator.new do |enum|
-      @handle.each do |line|
-        if line[0].chr == '>'
-          enum.yield Fasta.new(:name => header, :sequence => sequence) if sequence
-          sequence = ''
-          header = line[1..-1].strip
-        else
-          sequence << line.strip.tr(' ','')
-        end
-      end
-      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
-          params[:name] = line.strip[1..-1]
-        when 1
-          params[:sequence] = line.strip
-        when 2
-          nil
-        when 3
-          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|
-        line = line.strip.split("\t")
-        record = QSEQ.new(
-          :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]
-        )
-        enum.yield record
-      end
-    end
+    @iterator.each(&block)
   end
 end
 

data/readme.md

@@ -14,7 +14,7 @@ Supported Formats:
 
 ## Installation
 
-With Ruby 1.9.2 or better:
+With Ruby 1.8.7 or better:
 
 `gem install dna`
 
@@ -24,8 +24,10 @@ With Ruby 1.9.2 or better:
 
 require 'dna'
 
+# format detected automatically by inspecting the contents of the file.
+
 File.open('sequences.fasta') do |handle|
-  records = Dna.new handle, format: 'fastq'
+  records = Dna.new handle
   
   records.each do |record|
     puts record.length
@@ -33,7 +35,7 @@ File.open('sequences.fasta') do |handle|
 end
 
 File.open('sequences.fastq') do |handle|
-  records = Dna.new handle, format: 'fastq'
+  records = Dna.new handle
 
   records.each do |record|
     puts record.quality
@@ -41,7 +43,7 @@ File.open('sequences.fastq') do |handle|
 end
 
 File.open('sequences.qseq') do |handle|
-  records = Dna.new handle, format: 'qseq'
+  records = Dna.new handle
   puts records.first.inspect
 end
 ```

data/spec/dna_spec.rb

@@ -3,9 +3,9 @@ require 'spec_helper'
 describe Dna do
   include_context "parser stuff"
 
-  let(:fasta) { Dna.new @fasta_file }
-  let (:fastq) { Dna.new @fastq_file }
-  let (:qseq) { Dna.new @qseq_file }
+  let(:fasta) { Dna.new(@fasta_file) }
+  let(:fastq) { Dna.new @fastq_file }
+  let(:qseq) { Dna.new @qseq_file }
 
   it 'can auto-detect fasta format' do
     fasta.format == 'fasta'

metadata

@@ -1,22 +1,32 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: dna
-version: !ruby/object:Gem::Version
-  version: 0.0.5
+version: !ruby/object:Gem::Version 
+  hash: 19
   prerelease: 
+  segments: 
+  - 0
+  - 0
+  - 6
+  version: 0.0.6
 platform: ruby
-authors:
+authors: 
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2010-02-10 00:00:00.000000000 Z
+
+date: 2012-04-05 00:00:00 Z
 dependencies: []
+
 description: for parsing various types of DNA sequence files
 email: harekrishna@gmail.com
 executables: []
+
 extensions: []
+
 extra_rdoc_files: []
-files:
+
+files: 
 - lib/dna.rb
 - spec/dna_spec.rb
 - spec/record_spec.rb
@@ -24,26 +34,36 @@ files:
 - readme.md
 homepage: http://github.com/audy/dna
 licenses: []
+
 post_install_message: 
 rdoc_options: []
-require_paths:
+
+require_paths: 
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
 requirements: []
+
 rubyforge_project: 
-rubygems_version: 1.8.15
+rubygems_version: 1.8.21
 signing_key: 
 specification_version: 3
 summary: DNA sequence parser
 test_files: []
+