added write_sam biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2095 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/write_sam b/bp_bin/write_sam
new file mode 100755 (executable)
index 0000000..17a6536
--- /dev/null
+++ b/bp_bin/write_sam
@@ -0,0 +1,67 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2013 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write sequences from stream in SAM format.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/sam'
+
+casts = []
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'data_out',  :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'compress',  :short=>'Z', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  if options[:data_out]
+    if options[:compress]
+      io_out = Zlib::GzipWriter.open(options[:data_out])
+    else
+      io_out = File.open(options[:data_out], 'w')
+    end
+  else
+    io_out = $stdout
+  end
+
+  input.each do |record|
+    if sam = Sam.new_bp(record)
+      io_out.puts sam
+    end
+
+    output.puts record unless options[:no_stream]
+  end
+
+  io_out.close
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__