Module: Scaffolder::Test::Helpers

Defined in:
lib/scaffolder/test/helpers.rb

Instance Method Summary collapse

Instance Method Details

#generate_gff3_file(records, file = Tempfile.new("gff")) ⇒ Object 



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# 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) ⇒ Object 



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# 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")) ⇒ Object 



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# 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")) ⇒ Object 



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# 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