cleaning up digest.rb

[biopieces.git] / bp_bin / digest_seq

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 56fa32253692642641c88f80d50216851c7364cd..fa6cf8ef412df1b28199e050c94f612ac32a8cda 100755 (executable)
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -28,7 +28,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
 require 'maasha/biopieces'
 require 'maasha/seq'
 
@@ -41,11 +40,11 @@ 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(record[:SEQ_NAME], record[:SEQ])
+      seq    = Seq.new_bp(record)
       digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
 
       digest.each do |subseq|
-        new_record            = subseq.to_bp
+        new_record = subseq.to_bp
 
         if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
           s_beg = $1
@@ -63,7 +62,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   end
 end
 
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<