changed blast_seq_pair to do multiple pairs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2125 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index d612a6cdc06b7c3ead49bdae36945b5ae3f01e66..ca1d543533a8056f62d0eeff6ed22cdc92f2fbef 100755 (executable)
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -79,7 +79,7 @@ class Blast
   def each
     record = {}
 
-    File.open(@outfile, mode="r") do |ios|
+    File.open(@outfile, 'r') do |ios|
       ios.each_line do |line|
         if line !~ /^#/
           fields = line.chomp.split("\t")
@@ -155,8 +155,8 @@ infile1 = File.join(tmpdir, "in1.fna")
 infile2 = File.join(tmpdir, "in2.fna")
 outfile = File.join(tmpdir, "blast.out")
 
-got1    = false
-got2    = false
+got1    = nil
+got2    = nil
 type1   = ""
 type2   = ""
 
@@ -167,36 +167,37 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     if record[:SEQ_NAME] and record[:SEQ]
       seq = Seq.new_bp(record)
 
-      unless got1
-        Fasta.open(infile1, mode="w") do |fasta_io|
+      if got1.nil?
+        Fasta.open(infile1, "w") do |fasta_io|
           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|
+      elsif got2.nil?
+        Fasta.open(infile2, "w") do |fasta_io|
           fasta_io.puts seq.to_fasta
         end
 
         got2  = true
         type2 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
       end
-    end
-  end
 
-  if got1 and got2
-    blast = Blast.new(infile1, infile2, outfile)
-    blast.program_set(type1, type2, options[:program])
-    blast.run(options)
+      if got1 and got2
+        blast = Blast.new(infile1, infile2, outfile)
+        blast.program_set(type1, type2, options[:program])
+        blast.run(options)
 
-    blast.each do |record|
-      output.puts record
+        blast.each do |new_record|
+          output.puts new_record
+        end
+
+        got1 = nil
+        got2 = nil
+      end
     end
   end
+
 end