added xy-coord extraction code to sff.rb

[biopieces.git] / bp_bin / digest_seq

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 3fab531b4249cd144a5092cb58eb15c4d2b29d87..9fe81e9b83ad60162abc7711b95a3465182a865e 100755 (executable)
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Splits sequences in the stream at a given restriction enzyme's cleavage points.
+# Split sequences in the stream at a given restriction enzyme's cleavage points.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -42,17 +42,25 @@ bp = Biopieces.new
 options = bp.parse(ARGV, casts)
 
 bp.each_record do |record|
-  bp.puts record
-
   if record.has_key? :SEQ_NAME and record.has_key? :SEQ
     seq    = Seq.new(record[:SEQ_NAME], record[:SEQ])
     digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
 
     digest.each do |subseq|
       new_record            = subseq.to_bp
+
+      if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
+        s_beg = $1
+        s_end = $2
+      end
+
+      new_record[:S_BEG]    = s_beg 
+      new_record[:S_END]    = s_end
       new_record[:REC_TYPE] = "DIGEST"
       bp.puts new_record
     end
+  else
+    bp.puts record
   end
 end