class Scaffolder::Tool::Sequence

Public Class Methods

description() click to toggle source
# File lib/scaffolder/tool/sequence.rb, line 8
def self.description
  "Generate the fasta output for the scaffold"
end

Public Instance Methods

execute() click to toggle source
# 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={}) click to toggle source
# 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) click to toggle source
# File lib/scaffolder/tool/sequence.rb, line 19
def sequence(scaffold)
  scaffold.map{|entry| entry.sequence}.join
end