adding bzip2 support in ruby

[biopieces.git] / bp_bin / assemble_seq_velvet

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index abe6bd59f76ea342de5130d6ef783c2d9c53306a..e2753ce91ad65023d47627bd1c372553075fb14e 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -101,7 +101,7 @@ class Velvet
     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
@@ -144,7 +144,7 @@ Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 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|
+  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)
@@ -161,7 +161,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
     kmer = file_contigs.match(/_\d+/)
 
-               Fasta.open(file_contigs, mode="r") do |fasta_io|
+               Fasta.open(file_contigs, "r") do |fasta_io|
                  fasta_io.each do |entry|
         entry.seq_name << "_kmer#{kmer}"
                          output.puts entry.to_bp