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]
record[:TYPE] = File.basename(outfile).sub(".fna", "").upcase
record[:SEQ_NAME].match(/(.+):\[(\d+),(\d+)\]$/)
record[:SEQ_NAME] = $1
- record[:PCR_BEG] = $2
- record[:PCR_END] = $3
+ record[:PCR_BEG] = $2.to_i
+ record[:PCR_END] = $3.to_i
if record[:PCR_BEG] > record[:PCR_END]
record[:PCR_BEG], record[:PCR_END] = record[:PCR_END], record[:PCR_BEG]