From 49160fe9cb5472914fc4596a27605898974212ed Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 10 May 2011 10:27:31 +0000 Subject: [PATCH] added procedure switch to find_genes git-svn-id: http://biopieces.googlecode.com/svn/trunk@1391 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/find_genes | 3 ++- code_ruby/Maasha/lib/prodigal.rb | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/bp_bin/find_genes b/bp_bin/find_genes index 16cba9b..f0d64c8 100755 --- 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 1a1fd55..9ddbf79 100644 --- 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}" -- 2.39.5