adding bzip2 support in ruby

[biopieces.git] / bp_bin / assemble_seq_ray

diff --git a/bp_bin/assemble_seq_ray b/bp_bin/assemble_seq_ray
index fbef82aedd72fba3bc268adaba38fba6eed4eaa0..87d25f343bdb8acdbc6b828e8b7648f7029f0b2f 100755 (executable)
--- 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