X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fassemble_seq_ray;h=87d25f343bdb8acdbc6b828e8b7648f7029f0b2f;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=fbef82aedd72fba3bc268adaba38fba6eed4eaa0;hpb=b1fadc0ce9224b6a13f8deae332bb902a54c65af;p=biopieces.git

diff --git a/bp_bin/assemble_seq_ray b/bp_bin/assemble_seq_ray
index fbef82a..87d25f3 100755
--- a/bp_bin/assemble_seq_ray
+++ b/bp_bin/assemble_seq_ray
@@ -100,7 +100,7 @@ class Ray
     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
@@ -139,7 +139,7 @@ Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 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|
       if record[:SEQ_NAME] and record[:SEQ]
         seq = Seq.new_bp(record)
@@ -154,7 +154,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 		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