class Bio::Assembly::Ace::Read

extend Read class to add ace specific methods for read objects

Attributes

base_sequences[RW]

Public Instance Methods

add_base_sequence(from, to, read_name) click to toggle source
# File lib/bio-assembly/ace.rb, line 218
def add_base_sequence(from, to, read_name)
  @base_sequences = Array.new if @base_sequences.nil?
  @base_sequences.push BaseSequence.new(from, to, read_name)
end
to_ace() click to toggle source
# File lib/bio-assembly/ace.rb, line 178
def to_ace
  ace += ""
  # holds BS data for reads
  bs_str = ""
  # holds RD, QA, and DS data for reads
  rest_str = ""
  ace += to_ace_af
  bs_str += to_ace_bs
  rest_str = to_ace_rest

  # compile data in correct order
  ace += bs_str
  ace += "\n"
  ace += rest_str
  ace
end
to_ace_af() click to toggle source
# File lib/bio-assembly/ace.rb, line 205
def to_ace_af
  ['AF', name, orientation, from].join(' ') + "\n"
end
to_ace_bs() click to toggle source
# File lib/bio-assembly/ace.rb, line 195
def to_ace_bs
  bs_str = ""
  unless base_sequences.nil?
    base_sequences.each do |bs|
      bs_str += ['BS', bs.from, bs.to, bs.read_name].join(' ') + "\n"
    end
  end
  bs_str
end
to_ace_rest() click to toggle source
# File lib/bio-assembly/ace.rb, line 209
def to_ace_rest
  rest_str = ""
  rest_str += ['RD', name, num_bases, 0, 0].join(' ') + "\n"
  rest_str += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n")  + "\n"
  rest_str += ['QA', clear_range_from, clear_range_to, clear_range_from, clear_range_to].join(' ') + "\n"
  rest_str += ['DS', 'CHROMAT_FILE:', name, 'PHD_FILE:', "#{name}.phd.1", 'TIME:', Time.now].join(' ') + "\n"
  rest_str
end