BioRuby Assembly Plugin

I recently had the need to work with some Ace files and found that BioRuby didn't have an Ace parser. Instead of falling back to BioPerl, I decided to write a quick BioRuby plugin.   Install or fork on github ( https://github.com/chmille4/bioruby-assembly ).

	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

view raw BioRuby_Ace_Parser_Example.rb hosted with ❤ by GitHub