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)
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# 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()
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# 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()
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# File lib/bio-assembly/ace.rb, line 205 def to_ace_af ['AF', name, orientation, from].join(' ') + "\n" end
to_ace_bs()
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# 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()
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# 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