class Scaffolder::Tool::Sequence
Public Class Methods
description()
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# File lib/scaffolder/tool/sequence.rb, line 8 def self.description "Generate the fasta output for the scaffold" end
Public Instance Methods
execute()
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# File lib/scaffolder/tool/sequence.rb, line 12 def execute s = sequence(scaffold) Bio::Sequence.new(s).output(:fasta,:header => header(s,@settings)) end
Private Instance Methods
header(sequence,opts={})
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# File lib/scaffolder/tool/sequence.rb, line 23 def header(sequence,opts={}) header = Array.new header << opts[:definition] if opts[:definition] if opts[:'with-sequence-digest'] digest = Digest::SHA1.hexdigest(sequence) header << "[sha1=#{digest}]" end header * ' ' end
sequence(scaffold)
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# File lib/scaffolder/tool/sequence.rb, line 19 def sequence(scaffold) scaffold.map{|entry| entry.sequence}.join end