added digest_seq Biopiece

[biopieces.git] / bp_bin / digest_seq

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
new file mode 100755 (executable)
index 0000000..3fab531
--- /dev/null
+++ b/bp_bin/digest_seq
@@ -0,0 +1,63 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Splits sequences in the stream at a given restriction enzyme's cleavage points.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+require 'fasta'
+require 'seq'
+
+casts = []
+casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cut_pos', :short=>'c', :type=>'int',    :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  bp.puts record
+
+  if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+    seq    = Seq.new(record[:SEQ_NAME], record[:SEQ])
+    digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
+
+    digest.each do |subseq|
+      new_record            = subseq.to_bp
+      new_record[:REC_TYPE] = "DIGEST"
+      bp.puts new_record
+    end
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__