Ace Parser For BioRuby

BioRuby_Ace_Parser_Example.rb

 require 'bio-assembly'
 
 # ace file path
 asm = Bio::Assembly.new("data.ace", :ace)
 
 # iterate through contigs (streams each contig)
 asm.each_contig do |contig|
   
   # print name and consensus seq
   puts contig.name
   puts contig.consensus_seq
   
   # iterate through reads
   contig.each_read do |read|
       
      # print name, sequence and orientation
      puts read.name
      puts read.seq
      puts read.orientation
      
      # print the postion of the read
      # in relation to the consensus seq
      puts read.from
      puts read.to
      
      # print the portion of the read
      # that was used to create the consensus
      puts read.clear_range_from
      puts read.clear_range_to
      
   end
   
   # grab the reads that make up a particular region of the contig
   reads_in_region = contig.find_reads_in_range(10, 50)
   
 end
 
 # experimental - output ace
 file = File.new('out.ace', 'w')
 file.puts asm.to_ace

Use BioRuby to Parse and Write Ace files