module Scaffolder::Test::Helpers

Public Instance Methods

generate_gff3_file(records,file = Tempfile.new("gff")) click to toggle source
# File lib/scaffolder/test/helpers.rb, line 32
def generate_gff3_file(records,file = Tempfile.new("gff"))
  gff = Bio::GFF::GFF3.new
  gff.records = records.map{|r| r.to_gff3_record}
  File.open(file.path,'w'){|out| out.print(gff) }
  file
end
generate_scaffold_files(entries) click to toggle source
# File lib/scaffolder/test/helpers.rb, line 12
def generate_scaffold_files(entries)
  [write_scaffold_file(entries),write_sequence_file(entries)]
end
write_scaffold_file(entries,file = Tempfile.new("scaffold")) click to toggle source
# File lib/scaffolder/test/helpers.rb, line 16
def write_scaffold_file(entries,file = Tempfile.new("scaffold"))
  File.open(file.path,'w') do |tmp|
    tmp.print(YAML.dump(entries.map{|e| e.to_hash }))
  end
  file
end
write_sequence_file(entries,file = Tempfile.new("sequence")) click to toggle source
# File lib/scaffolder/test/helpers.rb, line 23
def write_sequence_file(entries,file = Tempfile.new("sequence"))
  File.open(file.path,'w') do |tmp|
    entries.each do |entry|
      tmp.puts(entry.to_fasta) if entry.respond_to? :to_fasta
    end
  end
  file
end