bio-assembly

BioRuby plugin for parsing, writing, and maniuplating assembly data

Currently supports ACE and CAF formats

Install

gem install bio-assembly

Usage

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

Contributing to bio-assembly

Copyright © 2011 Chase Miller and Francesco Strozzi. See LICENSE.txt for further details.