X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fswapcase_seq;h=b1fafa2ccd74cafe9783c3c9008b141426331296;hb=af282a65d141826c15944437b07a0353dd14e79c;hp=cb1989cf9d1f10c4f0c6eef9c9048bea2062b707;hpb=4cf3dcf93cf69e4b3e29d59ed7dd81ee74f5e6cf;p=biopieces.git

diff --git a/bp_bin/swapcase_seq b/bp_bin/swapcase_seq
index cb1989c..b1fafa2 100755
--- a/bp_bin/swapcase_seq
+++ b/bp_bin/swapcase_seq
@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2011 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -24,22 +24,20 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Swap lowercase sequence to uppercase and visa versa for all sequences in the stream.
+# Swap lower case sequence to uppercase and visa versa for all sequences in the stream.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
+require 'maasha/biopieces'
 
-casts = []
+options = Biopieces.options_parse(ARGV)
 
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
-
-bp.each_record do |record|
-  record[:SEQ].swapcase! if record.has_key? :SEQ
-  bp.puts record
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    record[:SEQ].swapcase! if record[:SEQ]
+    output.puts record
+  end
 end