added split_pair_seq biopiece

[biopieces.git] / bp_bin / blast_seq_pair

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index 5c4c678a4bbc7f89eb25aeb82f2d8a1ca2e3dfe4..d612a6cdc06b7c3ead49bdae36945b5ae3f01e66 100755 (executable)
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -121,14 +121,14 @@ class Blast
   def program_choose(type1, type2)
     program = ""
 
-    if type1 == 'protein'
-      if type2 == 'protein'
+    if type1 == :protein
+      if type2 == :protein
         program = 'blastp'
       else
         program = 'tblastn'
       end
     else
-      if type2 == 'protein'
+      if type2 == :protein
         program = 'blastx'
       else
         program = 'blastn'
@@ -164,19 +164,22 @@ 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
         type1 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
+        next
       end
 
       unless got2
         Fasta.open(infile2, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got2  = true