added prodigal.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1380 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/prodigal.rb b/code_ruby/Maasha/lib/prodigal.rb
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+++ b/code_ruby/Maasha/lib/prodigal.rb
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+# Copyright (C) 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 software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'genbank'
+
+# Class for running the Prodigal gene finder.
+# http://prodigal.ornl.gov/
+class Prodigal
+  include Enumerable
+
+  # Method to initialize a Prodigal object
+  # given a temporary infile, outfile and options hash.
+  def initialize(infile, outfile, options)
+    @infile  = infile
+    @outfile = outfile
+    @options = options
+  end
+
+  # Method to run Prodigal.
+  def run
+    commands = []
+    commands << "prodigal"
+    commands << "-c" if @options[:full]
+    commands << "-i #{@infile}"
+    commands << "-o #{@outfile}"
+
+    execute(commands, @options[:verbose])
+  end
+
+  # Method for iterating over the Prodigal results,
+  # which are in GenBank format.
+  def each
+    Genbank.open(@outfile, mode='r') do |gb|
+      gb.each do |entry|
+        yield entry
+      end
+    end
+  end
+
+  private
+
+  # Method to execute commands on the command line.
+  # TODO this wants to be in a module on its own.
+  def execute(commands, verbose = false)
+    commands.unshift "nice -n 19"
+    commands.push "> /dev/null 2>&1" unless verbose
+
+    command = commands.join(" ")
+
+    begin
+      system(command)
+      raise "Command failed: #{command}" unless $?.success?
+    rescue
+      $stderr.puts "Command failed: #{command}"
+    end
+  end
+end
+
+
+__END__