added mask_seq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1071 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/mask_seq b/bp_bin/mask_seq
new file mode 100755 (executable)
index 0000000..fe70a64
--- /dev/null
+++ b/bp_bin/mask_seq
@@ -0,0 +1,72 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Soft mask sequences in the stream based on Solexa/Illumina/Phred type quality scores.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+
+# Expading class Hash with possibly evil monkey patch.
+class Hash
+  # Soft masks sequence residues where the corresponding quality score
+  # is below a given cutoff.
+  def mask_seq!(cutoff, base)
+    if self.has_key? :SEQ and self.has_key? :SCORES
+      seq    = self[:SEQ].upcase
+      scores = self[:SCORES]
+      i      = 0
+
+      scores.each_char do |score|
+        seq[i] = seq[i].downcase if score.ord - base < cutoff
+        i += 1
+      end
+
+      self[:SEQ] = seq
+    end
+
+    self
+  end
+end
+
+casts = []
+casts << {:long=>'cutoff', :short=>'c', :type=>'int',  :mandatory=>false, :default=>20, :allowed=>nil,        :disallowed=>nil}
+casts << {:long=>'base',   :short=>'b', :type=>'uint', :mandatory=>false, :default=>64, :allowed=>"33,59,64", :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  bp.puts record.mask_seq!(options[:cutoff], options[:base])
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__