count = 0
n50 = 0
- Fasta.open(file, mode="r") do |fasta_io|
+ Fasta.open(file, "r") do |fasta_io|
fasta_io.each do |entry|
total += entry.length
lengths << entry.length
file_fasta = File.join(options[:directory], "sequence_in.fasta")
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(file_fasta, mode="w") do |fasta_io|
+ Fasta.open(file_fasta, "w") do |fasta_io|
input.each_record do |record|
- fasta_io.puts record
+ if record[:SEQ_NAME] and record[:SEQ]
+ seq = Seq.new_bp(record)
+
+ fasta_io.puts seq.to_fasta
+ end
end
end
ray.run
file_contigs = ray.pick_best_assembly
- Fasta.open(file_contigs, mode="r") do |fasta_io|
+ Fasta.open(file_contigs, "r") do |fasta_io|
fasta_io.each do |entry|
output.puts entry.to_bp
end