X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fpatscan_seq;h=1b533a9ebee71f22ed6b769371bcc7b607d4bcfa;hb=6b4c2afa4b4b581a9c36083a1d059e846ee4b560;hp=ef217c559298293d0fdec522e77b9d46c1af535e;hpb=1d849d14e996265619752ead2a5e35356b54cca1;p=biopieces.git

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index ef217c5..1b533a9 100755
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -46,7 +46,7 @@ class Patscan
   end
 
   # Method to run Patscan
-  def run(comp = nil, type = nil, max_mis = nil, max_hit = nil, verbose = nil)
+  def run(comp = nil, type = nil, max_hit = nil, max_mis = nil, verbose = nil)
     args = []
     args << "scan_for_matches"
     args << "-c"            if comp
@@ -146,14 +146,16 @@ Biopieces.open(options[:stream_in], tmp_file) do |input, output|
         record[:SEQ_NAME] = seq_name_count
         seq_name_count += 1
 
+        seq = Seq.new_bp(record)
+
         if seq_type.nil?
-          seq      = Seq.new("", record[:SEQ])
           seq_type = seq.type_guess
         end
+
+        fasta_io.puts seq.to_fasta
       end
 
       output.puts record
-      fasta_io.puts record
     end
   end
 end
@@ -180,6 +182,8 @@ Biopieces.open(tmp_file, options[:stream_out]) do |input, output|
 
             output.puts record
           end
+        else
+          output.puts record
         end
       else
         output.puts record