X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fclip_seq;h=44d1e508e1b007a0a8ae50b4ba67f37bc88bb20c;hb=8d375c58a048400bc06ce223bbb3315060b3b471;hp=4af564c9b487467f65f441f54864f5ccad06509f;hpb=a66f9359480be4e44b608c682c355e6a725b051c;p=biopieces.git

diff --git a/bp_bin/clip_seq b/bp_bin/clip_seq
index 4af564c..44d1e50 100755
--- a/bp_bin/clip_seq
+++ b/bp_bin/clip_seq
@@ -29,32 +29,35 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
+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[:SEQ]
+      trim_beg = 0
+      trim_end = record[:SEQ].length
 
-bp.each_record do |record|
-  if record.has_key? :SEQ
-    trim_beg = 0
-    trim_end = record[:SEQ].length
+      record[:SEQ] =~ /[^a-z]/
 
-    record[:SEQ] =~ /[^a-z]/
+      trim_beg = $`.length
 
-    trim_beg = $`.length
+      if record[:SEQ] =~ /[a-z]+$/
+        trim_end = $`.length
+      else
+        trim_end = record[:SEQ].length
+      end
 
-    record[:SEQ] =~ /[a-z]+$/
-    trim_end = $`.length
+      record[:SEQ]     = record[:SEQ][trim_beg ... trim_end]
+      record[:SEQ_LEN] = record[:SEQ].length
+      record[:SCORES]  = record[:SCORES][trim_beg ... trim_end] if record[:SCORES]
+    end
 
-    record[:SEQ]     = record[:SEQ][trim_beg ... trim_end]
-    record[:SEQ_LEN] = record[:SEQ].length
-    record[:SCORES]  = record[:SCORES][trim_beg ... trim_end] if record.has_key? :SCORES
+    output.puts record
   end
-
-  bp.puts record
 end