class GenomerPluginView::Fasta
Public Instance Methods
header(identifier)
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# File lib/genomer-plugin-view/fasta.rb, line 20 def header(identifier) (identifier + ' ' + header_flags).strip end
header_flags()
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# File lib/genomer-plugin-view/fasta.rb, line 28 def header_flags flags.map{|k,v| "[#{k}=#{v}]" }.join(' ') end
identifier()
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# File lib/genomer-plugin-view/fasta.rb, line 24 def identifier flags[:identifier] ? flags.delete(:identifier) : '.' end
run()
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# 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()
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# File lib/genomer-plugin-view/fasta.rb, line 32 def sequence scaffold.map{|entry| entry.sequence}.join end