BioRuby plugin for parsing, writing, and maniuplating assembly data
Currently supports ACE and CAF formats
gem install bio-assembly
require 'bio-assembly' # ace file path asm = Bio::Assembly.open("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
Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
Fork the project
Start a feature/bugfix branch
Commit and push until you are happy with your contribution
Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
Copyright © 2011 Chase Miller and Francesco Strozzi. See LICENSE.txt for further details.