options = Biopieces.options_parse(ARGV, casts)
tmpdir = Biopieces.mktmpdir
-tmpdir = "Tmp"
infile1 = File.join(tmpdir, "in1.fna")
infile2 = File.join(tmpdir, "in2.fna")
outfile = File.join(tmpdir, "blast.out")
output.puts record
if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ seq = Seq.new_bp(record)
+
unless got1
Fasta.open(infile1, mode="w") do |fasta_io|
- fasta_io.puts record
+ fasta_io.puts seq.to_fasta
end
got1 = true
unless got2
Fasta.open(infile2, mode="w") do |fasta_io|
- fasta_io.puts record
+ fasta_io.puts seq.to_fasta
end
got2 = true