# Save a pattern to file
def save_pattern(file)
- File.open(file, mode="w") do |ios|
+ File.open(file, "w") do |ios|
ios.puts self
end
end
raise ArgumentError, "no adaptor specified" unless options[:forward] or options[:reverse]
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(infile, mode="w") do |ios|
+ Fasta.open(infile, "w") do |ios|
input.each_record do |record|
output.puts record
outfiles = Pcr.new(tmpdir, infile, options).run
outfiles.each do |outfile|
- Fasta.open(outfile, mode="r") do |ios|
+ Fasta.open(outfile, "r") do |ios|
ios.each do |entry|
record = entry.to_bp
record[:REC_TYPE] = "PCR"