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- 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
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