class GenomerPluginView::Fasta

Public Instance Methods

header(identifier) click to toggle source
# File lib/genomer-plugin-view/fasta.rb, line 20
def header(identifier)
  (identifier + ' ' + header_flags).strip
end
header_flags() click to toggle source
# File lib/genomer-plugin-view/fasta.rb, line 28
def header_flags
  flags.map{|k,v| "[#{k}=#{v}]" }.join(' ')
end
identifier() click to toggle source
# File lib/genomer-plugin-view/fasta.rb, line 24
def identifier
  flags[:identifier] ? flags.delete(:identifier) : '.'
end
run() click to toggle source
# File lib/genomer-plugin-view/fasta.rb, line 5
def run
  if flags[:contigs]
    flags.delete(:contigs)

    sequence.
      split(/[Nn]+/).
      map{|s| Bio::Sequence.new(s) }.
      each_with_index.
      map{|s,i| s.output(:fasta,:header => header(sprintf("contig%05d",i+1))) }.
      join
  else
    Bio::Sequence.new(sequence).output(:fasta,:header => header(identifier))
  end
end
sequence() click to toggle source
# File lib/genomer-plugin-view/fasta.rb, line 32
def sequence
  scaffold.map{|entry| entry.sequence}.join
end