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@chmille4
Created October 7, 2010 15:36
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Ace Parser For BioRuby
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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chmille4 commented Oct 7, 2010

Use BioRuby to Parse and Write Ace files

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