casts = []
casts << {:long=>'program', :short=>'p', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>ok_programs, :disallowed=>nil}
-casts << {:long=>'e_val', :short=>'e', :type=>'float', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'e_val', :short=>'e', :type=>'float', :mandatory=>false, :default=>10.0, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'filter', :short=>'f', :type=>'string', :mandatory=>false, :default=>'no', :allowed=>'yes,no', :disallowed=>nil}
casts << {:long=>'megablast', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'no_gaps', :short=>'G', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
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
type1 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
+ next
end
unless got2
Fasta.open(infile2, mode="w") do |fasta_io|
- fasta_io.puts record
+ fasta_io.puts seq.to_fasta
end
got2 = true