added clip_adaptor biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1339 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/clip_adaptor b/bp_bin/clip_adaptor
new file mode 100755 (executable)
index 0000000..4399743
--- /dev/null
+++ b/bp_bin/clip_adaptor
@@ -0,0 +1,54 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Clip adaptor sequences in the stream based on ADAPTOR_POS key.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+
+casts = []
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  if record.has_key? :SEQ and record.has_key? :ADAPTOR_POS
+    record[:SEQ]     = record[:SEQ][0 ... record[:ADAPTOR_POS].to_i]
+    record[:SCORES]  = record[:SCORES][0 ... record[:ADAPTOR_POS].to_i] if record[:SCORES]
+    record[:SEQ_LEN] = record[:SEQ].length
+  end
+
+  bp.puts record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__