casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>true, :default=>31, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list', :mandatory=>true, :default=>cov_cutoffs, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'exp_cov', :short=>'e', :type=>'float', :mandatory=>true, :default=>'auto', :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'clean', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean', :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
file_fasta = File.join(options[:directory], "sequence_in.fna")
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(file_fasta, mode="w") do |fasta_io|
- input.each_record do |record|
- fasta_io.puts record
- end
+ Fasta.open(file_fasta, mode="w") do |fasta_io|
+ input.each_record do |record|
+ if record[:SEQ_NAME] and record[:SEQ]
+ seq = Seq.new_bp(record)
+ fasta_io.puts seq.to_fasta
+ end
+ end
end
unless File.size(file_fasta) == 0