X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=bp_bin%2Fclip_adaptor;h=1bf6bf5240a61f374ec4ac9bed8d7e6e51aa001f;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=43997436e2e714129b2d544933e439e07661d0ed;hpb=553bbe1c3745e009c8914017d6ae202828c5fcef;p=biopieces.git

diff --git a/bp_bin/clip_adaptor b/bp_bin/clip_adaptor
index 4399743..1bf6bf5 100755
--- a/bp_bin/clip_adaptor
+++ b/bp_bin/clip_adaptor
@@ -29,22 +29,33 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
+require 'maasha/biopieces'
+require 'maasha/seq'
 
 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[:SEQ] and (record[:ADAPTOR_POS_LEFT] or record[:ADAPTOR_POS_RIGHT])
+      entry = Seq.new_bp(record)
 
-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
-  end
+      if record[:ADAPTOR_POS_RIGHT]
+        entry = entry[0 ... record[:ADAPTOR_POS_RIGHT].to_i]
+      end
+
+      if record[:ADAPTOR_POS_LEFT]
+        if record[:ADAPTOR_POS_LEFT].to_i + record[:ADAPTOR_LEN_LEFT].to_i < entry.length
+          entry = entry[record[:ADAPTOR_POS_LEFT].to_i + record[:ADAPTOR_LEN_LEFT].to_i .. -1]
+        end
+      end
 
-  bp.puts record
+      record.merge! entry.to_bp
+    end
+
+    output.puts record
+  end
 end