dna 0.0.0 → 0.0.1

data/lib/dna.rb

@@ -3,24 +3,102 @@ class Dna # iterator
   
   def initialize(handle, args={})
     @handle = handle
+    @format = args[:type].to_sym
+    
+    @iterator = 
+      case @format
+      when :fasta
+        fasta_parser
+      when :fastq
+        fastq_parser
+      when :qseq
+        qseq_parser
+      else
+        raise "#{@type} not supported."
+      end
   end
   
-  def each
-    sequence, header = nil, nil
-    @handle.each do |line|
-      if line[0].chr == '>'
-        yield Dna.new(:name => header, :sequence => sequence) if sequence
-        sequence = ''
-        header = line[1..-1].strip
+  def each &block
+    @iterator.each do |r|
+      if block_given?
+        block.call r
       else
-        sequence << line.strip.tr(' ','')
+        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|
+      @handle.each do |line|
+        n = c.next
+        case n
+        when 0
+          header = line.strip
+        when 1
+          sequence = line.strip
+        when 2
+          nil
+        when 3
+          quality = line.strip
+          enum.yield Fastq.new(name: header, sequence: sequence, quality: quality)
+        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
-    yield Dna.new(:name => header, :sequence => sequence) 
   end
 end
 
 class Record # nucleotide record
+  def length
+    @sequence.length
+  end
+end
+
+##
+# Fasta record
+#
+class Fasta < Record
   attr_accessor :name, :sequence
   
   def initialize(args={})
@@ -31,8 +109,50 @@ class Record # nucleotide record
   def to_s
     ">#{@name}\n#{@sequence}\n"
   end
+end
+
+##
+# Fastq record
+#
+class Fastq < Record
+  attr_accessor :name, :sequence, :format, :quality
   
-  def length
-    @sequence.length
+  def initialize(args={})
+    @name = args[:name]
+    @sequence = args[:sequence]
+    @quality = args[:quality]
+  end
+  
+  def to_s
+    "@#{@name}\n#{@sequence}\n+#{@name}\n#{@quality}"
+  end
+end
+
+##
+# QSEQ record
+#
+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]
+  end
+  
+  def to_s
+    [@machine, @run, @lane, @tile, @x, @y, @index, @read_no, @sequence, @quality, @filtered].join("\t")
+  end
+  
+  def header
+    [@machine, @run, @lane, @tile, @x, @y, @index, @read_no, @sequence, @quality, @filtered].join(':')
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dna
 version: !ruby/object:Gem::Version
-  version: 0.0.0
+  version: 0.0.1
   prerelease: 
 platform: ruby
 authors: