class Bio::Assembly::Ace::Contig
extend contig class and write ace specific methods for contig objects
Public Instance Methods
to_ace()
click to toggle source
# File lib/bio-assembly/ace.rb, line 140 def to_ace ace = "" ace += ['CO', name, num_bases, num_reads, num_base_segments, orientation].join(' ') + "\n" ace += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n") + "\n" ace += "BQ\n" last_stop = quality.size - 1 (quality.size/50+1).times do |i| start = i * 50 stop = (i+1) * 50 - 1 stop = last_stop if stop > last_stop ace += ' ' + quality[start..stop].join(' ') + "\n" end ace += "\n" # holds BS data for reads bs_str = "" # holds RD, QA, and DS data for reads rest_str = "" @reads.values.sort.each do |read| ace += read.to_ace_af bs_str += read.to_ace_bs rest_str += read.to_ace_rest end # compile data in correct order ace += bs_str ace += "\n" ace += rest_str ace end