Class: Bio::Assembly::Ace::Contig

Inherits:
Contig
  • Object
show all
Defined in:
lib/bio-assembly/ace.rb

Overview

extend contig class and write ace specific methods for contig objects

Instance Attribute Summary

Attributes inherited from Contig

#from, #name, #orientation, #quality, #reads, #seq, #to

Instance Method Summary collapse

Methods inherited from Contig

#add_read, #each_read, #find_read_by_name, #find_reads_in_range, #initialize, #num_base_segments, #num_bases, #num_reads

Constructor Details

This class inherits a constructor from Bio::Assembly::Contig

Instance Method Details

#to_ace ⇒ Object 



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# 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