fixed seq qual length check

[biopieces.git] / bp_bin / swapcase_seq

diff --git a/bp_bin/swapcase_seq b/bp_bin/swapcase_seq
index 62a69796b04e50b53ab529fd951e7db976d21758..b1fafa2ccd74cafe9783c3c9008b141426331296 100755 (executable)
--- a/bp_bin/swapcase_seq
+++ b/bp_bin/swapcase_seq
@@ -1,40 +1,47 @@
 #!/usr/bin/env ruby
 
-require 'optparse'
-require 'pp'
+# Copyright (C) 2007-2011 Martin A. Hansen.
 
-options = {}
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
 
-optparse = OptionParser.new do |opts|
-  opts.on( '-?', '--help', 'Display this screen' ) do
-               biopiece = $0.split( "/" ).last
-               exec "print_wiki --data_in #{ ENV[ 'BP_DIR' ] }/bp_usage/#{ biopiece }.wiki --help"
-    exit
-  end
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
 
-       opts.on( '-v', '--verbose' ) do
-               options[ :verbose ] = true
-       end
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
-       opts.on( '-I', '--stream_in FILE', Time ) do |arg|
-               options[:stream_in] = arg
-       end
+# http://www.gnu.org/copyleft/gpl.html
 
-#      opts.on( '-I', '--stream_in FILE', "Mandatory argument" ) do |arg|
-#              options[:stream_in] = arg
-#      end
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Swap lower case sequence to uppercase and visa versa for all sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-       opts.on( '-O', '--stream_in FILE', "Mandatory argument" ) do |arg|
-               options[:stream_out] = arg
-       end
-end
 
-optparse.parse!
+require 'maasha/biopieces'
 
-pp "Options:", options
-pp "ARGV:", ARGV
+options = Biopieces.options_parse(ARGV)
 
-if ARGV.length == 0 then
-       biopiece = $0.split( "/" ).last
-       exec "print_wiki --data_in #{ ENV[ 'BP_DIR' ] }/bp_usage/#{ biopiece }.wiki"
+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
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__