From da18acf38dd939cdec558c919e53dd966c83ce1f Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 13 Jul 2012 13:52:36 +0000
Subject: [PATCH] added find_orfs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1867 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/find_orfs | 70 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100755 bp_bin/find_orfs

diff --git a/bp_bin/find_orfs b/bp_bin/find_orfs
new file mode 100755
index 0000000..868665d
--- /dev/null
+++ b/bp_bin/find_orfs
@@ -0,0 +1,70 @@
+#!/usr/bin/env ruby
+
+# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Determine the frequencies for k-mers in sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+require 'maasha/seq'
+
+casts = []
+casts << {:long=>'start_codons',  :short=>'s', :type=>'list', :mandatory=>true,  :default=>"AUG,GUG",     :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'stop_codons',   :short=>'S', :type=>'list', :mandatory=>true,  :default=>"UAA,UGA,UAG", :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'min_size',      :short=>'m', :type=>'uint', :mandatory=>true,  :default=>50,            :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'max_size',      :short=>'M', :type=>'uint', :mandatory=>true,  :default=>10_000,        :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'non_redundant', :short=>'r', :type=>'flag', :mandatory=>false, :default=>nil,           :allowed=>nil, :disallowed=>'0'}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SEQ]
+      entry = Seq.new_bp(record)
+
+      entry.each_orf(options[:min_size], options[:max_size], options[:start_codons], options[:stop_codons], options[:non_redundant]) do |orf, orf_beg, orf_end|
+        new_record = {}
+        new_record[:REC_TYPE] = "ORF"
+        new_record.merge!(orf.to_bp)
+        new_record[:S_BEG] = orf_beg
+        new_record[:S_END] = orf_end
+
+        output.puts new_record
+      end
+
+      exit
+    end
+
+    output.puts record
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-- 
2.39.5