adding bzip2 support in ruby

[biopieces.git] / bp_bin / pcr_seq

diff --git a/bp_bin/pcr_seq b/bp_bin/pcr_seq
index 09e626983184e9a14970c894989ed06a9f1e4db0..6afbb343f3e497595261f4cd785a558ff0ce97b9 100755 (executable)
--- a/bp_bin/pcr_seq
+++ b/bp_bin/pcr_seq
@@ -146,7 +146,7 @@ class Pattern
 
   # Save a pattern to file
   def save_pattern(file)
-    File.open(file, mode="w") do |ios|
+    File.open(file, "w") do |ios|
       ios.puts self
     end
   end
@@ -173,7 +173,7 @@ end
 
 raise ArgumentError, "no adaptor specified" unless options[:forward] or options[:reverse]
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  Fasta.open(infile, mode="w") do |ios|
+  Fasta.open(infile, "w") do |ios|
     input.each_record do |record|
       output.puts record
 
@@ -187,7 +187,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   outfiles = Pcr.new(tmpdir, infile, options).run
 
   outfiles.each do |outfile|
-    Fasta.open(outfile, mode="r") do |ios|
+    Fasta.open(outfile, "r") do |ios|
       ios.each do |entry|
         record = entry.to_bp
         record[:REC_TYPE] = "PCR"