find_pairs added

[biopieces.git] / bp_bin / digest_seq

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index fa6cf8ef412df1b28199e050c94f612ac32a8cda..b4451342da493e456e0f25e9521fa7371a7f8fdd 100755 (executable)
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -40,11 +40,10 @@ options = Biopieces.options_parse(ARGV, casts)
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
-      seq    = Seq.new_bp(record)
-      digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
+      seq = Seq.new_bp(record)
 
-      digest.each do |subseq|
-        new_record = subseq.to_bp
+      seq.each_digest(options[:pattern].to_s, options[:cut_pos]) do |digest|
+        new_record = digest.to_bp
 
         if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
           s_beg = $1
@@ -54,6 +53,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         new_record[:S_BEG]    = s_beg 
         new_record[:S_END]    = s_end
         new_record[:REC_TYPE] = "DIGEST"
+
         output.puts new_record
       end
     else