removed debug message

[biopieces.git] / bp_bin / digest_seq

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 7399ae0621b9101210960a2c2946e90138175128..2aa9ff9837fded6ad832d44fffacf99b08f96742 100755 (executable)
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -28,9 +28,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
 require 'maasha/biopieces'
-require 'maasha/fasta'
 require 'maasha/seq'
 
 casts = []
@@ -41,12 +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(record[:SEQ_NAME], record[:SEQ])
-      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
@@ -56,6 +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
@@ -64,7 +62,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   end
 end
 
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<