Contents

require 'bio'

class Bio::FlatFile
  include Enumerable
end

class Bio::FastaFormat
  alias_method :header, :definition
  alias_method :sequence, :seq
end

module Ms
  # A convenience class for working with fasta formatted sequence databases.
  # the file which includes this class also includes Enumerable with
  # Bio::FlatFile so you can do things like this:
  #
  #     accessions = Ms::Fasta.open("file.fasta") do |fasta| 
  #       fasta.map(&:accession)
  #     end
  # 
  # A few aliases are added to Bio::FastaFormat
  #
  #     entry.header == entry.definition
  #     entry.sequence == entry.seq
  #
  # Ms::Fasta.new accepts both an IO object or a String (a fasta formatted
  # string itself)
  #
  #     # taking an io object:
  #     File.open("file.fasta") do |io| 
  #       fasta = Ms::Fasta.new(io)
  #       ... do something with it
  #     end
  #     # taking a string
  #     string = ">id1 a simple header\nAAASDDEEEDDD\n>id2 header again\nPPPPPPWWWWWWTTTTYY\n"
  #     fasta = Ms::Fasta.new(string)
  #     (simple, not_simple) = fasta.partition {|entry| entry.header =~ /simple/ }
  module Fasta

    # opens the flatfile and yields a Bio::FlatFile object
    def self.open(file, &block)
      Bio::FlatFile.open(Bio::FastaFormat, file, &block)
    end

    # yields each Bio::FastaFormat object in turn
    def self.foreach(file, &block)
      Bio::FlatFile.open(Bio::FastaFormat, file) do |fasta|
        fasta.each(&block)
      end
    end

    # takes an IO object or a string that is the fasta data itself
    def self.new(io)
      io = StringIO.new(io) if io.is_a?(String)
      Bio::FlatFile.new(Bio::FastaFormat, io)
    end

  end
end

Version data entries

6 entries across 6 versions & 1 rubygems

Version	Path
ms-core-0.0.17	lib/ms/fasta.rb
ms-core-0.0.16	lib/ms/fasta.rb
ms-core-0.0.14	lib/ms/fasta.rb
ms-core-0.0.13	lib/ms/fasta.rb
ms-core-0.0.12	lib/ms/fasta.rb
ms-core-0.0.11	lib/ms/fasta.rb