X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fdigest_seq;h=2aa9ff9837fded6ad832d44fffacf99b08f96742;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=e3a7c4fb4ebfc66a3666bd4569f4f275065f57e9;hpb=a0cc93e32e6f8ece751b2b653bac0ebbe5f40b37;p=biopieces.git

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index e3a7c4f..2aa9ff9 100755
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -30,7 +30,6 @@
 
 require 'maasha/biopieces'
 require 'maasha/seq'
-require 'maasha/digest'
 
 casts = []
 casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
@@ -40,12 +39,11 @@ 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_bp(record)
-      digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
+    if record[:SEQ_NAME] and record[:SEQ]
+      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
@@ -55,6 +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