added max_diversity swith to findsim.rb

[biopieces.git] / bp_bin / clip_adaptor

diff --git a/bp_bin/clip_adaptor b/bp_bin/clip_adaptor
index 2056f2d31a1fadfe960931fcc16898a460a5d427..5cb2fa5ae083756c629849d08502c3ce9711386a 100755 (executable)
--- a/bp_bin/clip_adaptor
+++ b/bp_bin/clip_adaptor
@@ -33,18 +33,18 @@ require 'maasha/biopieces'
 
 casts = []
 
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
 
-options = bp.parse(ARGV, casts)
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record.has_key? :SEQ and record.has_key? :ADAPTOR_POS
+      record[:SEQ]     = record[:SEQ][0 ... record[:ADAPTOR_POS].to_i]
+      record[:SCORES]  = record[:SCORES][0 ... record[:ADAPTOR_POS].to_i] if record[:SCORES]
+      record[:SEQ_LEN] = record[:SEQ].length
+    end
 
-bp.each_record do |record|
-  if record.has_key? :SEQ and record.has_key? :ADAPTOR_POS
-    record[:SEQ]     = record[:SEQ][0 ... record[:ADAPTOR_POS].to_i]
-    record[:SCORES]  = record[:SCORES][0 ... record[:ADAPTOR_POS].to_i] if record[:SCORES]
-    record[:SEQ_LEN] = record[:SEQ].length
+    output.puts record
   end
-
-  bp.puts record
 end