added procedure switch to find_genes

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1391 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index 16cba9ba59573c37690b6a5297ce9e160388c67e..f0d64c8365300b3c970dd43fd6f6f7c1ed67f9e1 100755 (executable)
--- a/bp_bin/find_genes
+++ b/bp_bin/find_genes
@@ -34,7 +34,8 @@ require 'fasta'
 require 'prodigal'
 
 casts = []
-casts << {:long=>'full', :short=>'f', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'full', :short=>'f', :type=>'flag',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'full', :short=>'p', :type=>'procedure', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
 
 bp = Biopieces.new
 

diff --git a/code_ruby/Maasha/lib/prodigal.rb b/code_ruby/Maasha/lib/prodigal.rb
index 1a1fd552af5311caf9f8b3ce1bd0187aa6b81007..9ddbf79f62db23cf5d73f3a867933af48f0bd8e3 100644 (file)
--- a/code_ruby/Maasha/lib/prodigal.rb
+++ b/code_ruby/Maasha/lib/prodigal.rb
@@ -42,6 +42,7 @@ class Prodigal
     commands = []
     commands << "prodigal"
     commands << "-c" if @options[:full]
+    commands << "-p #{@options[:procedure]}"
     commands << "-i #{@infile}"
     commands << "-o #{@outfile}"