seq = Seq.new
seq.seq = primer
seq.type = 'dna'
- seq.revcomp
+ seq.reverse!.complement!
descriptor ? seq.seq + descriptor : seq.seq
end
infile = File.join(tmpdir, "in.fna")
if options[:forward_rc]
- options[:forward] = Seq.new("test", options[:forward_rc], 'dna').revcomp.seq
+ options[:forward] = Seq.new("test", options[:forward_rc], 'dna').reverse.complement.seq
end
if options[:reverse_rc]
- options[:reverse] = Seq.new("test", options[:reverse_rc], 'dna').revcomp.seq
+ options[:reverse] = Seq.new("test", options[:reverse_rc], 'dna').reverse.complement.seq
end
raise ArgumentError, "no adaptor specified" unless options[:forward] or options[:reverse]
input.each_record do |record|
output.puts record
- if record.has_key? :SEQ
+ if record[:SEQ]
entry = Seq.new_bp(record)
ios.puts entry.to_fasta
end