adding bzip2 support in ruby

[biopieces.git] / bp_bin / swapcase_seq

diff --git a/bp_bin/swapcase_seq b/bp_bin/swapcase_seq
index 06f6089a4d827fa83d274e93fbb22e2a882209f7..b1fafa2ccd74cafe9783c3c9008b141426331296 100755 (executable)
--- a/bp_bin/swapcase_seq
+++ b/bp_bin/swapcase_seq
@@ -1,37 +1,47 @@
 #!/usr/bin/env ruby
 
-require 'Maasha/biopieces'
-require 'getoptlong'
-
-options = GetoptLong.new(
-    [ '--help',       '-?', GetoptLong::NO_ARGUMENT ],
-    [ '--stream_in',  '-I', GetoptLong::REQUIRED_ARGUMENT ],
-    [ '--stream_out', '-O', GetoptLong::REQUIRED_ARGUMENT ],
-    [ '--verbose',    '-v', GetoptLong::NO_ARGUMENT ]
-)
-
-if ARGV.length == 0 then
-    biopiece = $0.split( "/" ).last
-    exec "print_wiki --data_in #{ ENV[ 'BP_DIR' ] }/bp_usage/#{ biopiece }.wiki"
-end
+# 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
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# 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.
+
+# 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.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-options.each do | opt, arg |
-    puts "option: #{ opt }   argument: #{ arg }"
-
-    case opt
-        when '--help'
-            biopiece = $0.split( "/" ).last
-            exec "print_wiki --data_in #{ ENV[ 'BP_DIR' ] }/bp_usage/#{ biopiece }.wiki --help"
-        when '--stream_in'
-            puts "Stream in"
-            stream = File.open( arg )
-        when '--stream_out'
-            puts "Stream out"
-        when '--verbose'
-            puts "blababnlbalbalbalbalab"
-    end
+# Swap lower case sequence to uppercase and visa versa for all sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+
+options = Biopieces.options_parse(ARGV)
+
+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
 
-bp_stream = BioPieces.new( "test.stream" )
 
-puts bp_stream.record_get
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__