class Scaffolder::Test::Sequence
Public Class Methods
new(options = {})
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# File lib/scaffolder/test/sequence.rb, line 6 def initialize(options = {}) @options = options end
Public Instance Methods
initialize_copy(source)
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Calls superclass method
# File lib/scaffolder/test/sequence.rb, line 10 def initialize_copy(source) super @options = @options.dup end
inserts(arg = nil)
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# File lib/scaffolder/test/sequence.rb, line 25 def inserts(arg = nil) return @options[:inserts] if arg.nil? @options[:inserts] ||= Array.new if arg.instance_of?(Array) arg.each {|a| @options[:inserts] << a} else @options[:inserts] << arg end return self end
to_fasta()
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# File lib/scaffolder/test/sequence.rb, line 47 def to_fasta fasta = Bio::Sequence.new(sequence).output(:fasta,:header => name) inserts.each_with_index do |insert,i| fasta << Bio::Sequence.new(insert[:sequence]).output(:fasta,:header => "insert#{i+1}") end if inserts fasta.strip end
to_hash()
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# File lib/scaffolder/test/sequence.rb, line 36 def to_hash hash = {'source' => name}.merge stringify_keys(@options) if @options[:inserts] hash['inserts'] = Array.new @options[:inserts].each_with_index do |insert,i| hash['inserts'] << {'source' => "insert#{i+1}"}.merge(stringify_keys(insert)) end end {'sequence' => hash} end
Private Instance Methods
stringify_keys(hash)
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# File lib/scaffolder/test/sequence.rb, line 57 def stringify_keys(hash) [:start,:stop,:reverse,:open,:close].inject(Hash.new) do |stringified,key| stringified[key.to_s] = hash[key] if hash[key] stringified end end