dna 0.0.0

data/lib/dna.rb

@@ -0,0 +1,38 @@
+class Dna # iterator
+  include Enumerable
+  
+  def initialize(handle, args={})
+    @handle = handle
+  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
+      else
+        sequence << line.strip.tr(' ','')
+      end
+    end
+    yield Dna.new(:name => header, :sequence => sequence) 
+  end
+end
+
+class Record # nucleotide record
+  attr_accessor :name, :sequence
+  
+  def initialize(args={})
+    @name = args[:name]
+    @sequence = args[:sequence]
+  end
+  
+  def to_s
+    ">#{@name}\n#{@sequence}\n"
+  end
+  
+  def length
+    @sequence.length
+  end
+end

metadata

@@ -0,0 +1,45 @@
+--- !ruby/object:Gem::Specification
+name: dna
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+  prerelease: 
+platform: ruby
+authors:
+- Austin G. Davis-Richardson
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2010-01-27 00:00:00.000000000 Z
+dependencies: []
+description: for parsing fasta files
+email: harekrishna@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/dna.rb
+homepage: http://github.com/audy/dna
+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: fasta parser
+test_files: []