X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fblast_seq_pair;h=1963eafc4b128d94579d6d02e86cddf14964962c;hb=5a9b7c80e4e4428e404575ed3c0290cde15a7402;hp=b6529fb4017a6c5d873747a7a26f8ab2560b0c1b;hpb=d8616c34c76ed72cd6cf290add6abcc4b8470994;p=biopieces.git

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index b6529fb..1963eaf 100755
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -151,7 +151,6 @@ casts << {:long=>'no_gaps',   :short=>'G', :type=>'flag',   :mandatory=>false, :
 options = Biopieces.options_parse(ARGV, casts)
 
 tmpdir  = Biopieces.mktmpdir
-tmpdir  = "Tmp"
 infile1 = File.join(tmpdir, "in1.fna")
 infile2 = File.join(tmpdir, "in2.fna")
 outfile = File.join(tmpdir, "blast.out")
@@ -165,10 +164,12 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     output.puts record
 
-    if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+    if record[:SEQ_NAME] and record[:SEQ]
+      seq = Seq.new_bp(record)
+
       unless got1
         Fasta.open(infile1, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got1  = true
@@ -178,7 +179,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
       unless got2
         Fasta.open(infile2, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got2  = true