adding bzip2 support in ruby

[biopieces.git] / bp_bin / analyze_assembly

diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly
index 3b9748db523c20c412ea21e52edd9c206402b25b..614a9e54d8e85bc00e84e2a6deab96049c0ddb5d 100755 (executable)
--- a/bp_bin/analyze_assembly
+++ b/bp_bin/analyze_assembly
@@ -50,10 +50,10 @@ tmpdir  = Biopieces.mktmpdir
 infile  = File.join(tmpdir, "in.fna")
 outfile = File.join(tmpdir, "out.prodigal")
 
-Fasta.open(infile, mode="w") do |fasta_output|
+Fasta.open(infile, "w") do |fasta_output|
   Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     input.each_record do |record|
-      if record.has_key? :SEQ
+      if record[:SEQ]
         seq = Seq.new_bp(record)
 
         total   += record[:SEQ].length