From 3f7bd9e4c1f304524c782279105a0335841a4a03 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 15 Aug 2012 13:34:14 +0000 Subject: [PATCH] made find_orfs run on DNA or RNA git-svn-id: http://biopieces.googlecode.com/svn/trunk@1896 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/find_orfs | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/bp_bin/find_orfs b/bp_bin/find_orfs index a1203ea..3deb53f 100755 --- a/bp_bin/find_orfs +++ b/bp_bin/find_orfs @@ -1,6 +1,6 @@ #!/usr/bin/env ruby -# Copyright (C) 2007-2011 Martin A. Hansen. +# Copyright (C) 2007-2012 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 @@ -32,12 +32,15 @@ require 'maasha/biopieces' require 'maasha/seq' +codons_start = "ATG,GTG,AUG,GUG" +codons_stop = "TAA,TGA,TAG,UAA,UGA,UAG" + 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=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'} +casts << {:long=>'start_codons', :short=>'s', :type=>'list', :mandatory=>true, :default=>codons_start, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'stop_codons', :short=>'S', :type=>'list', :mandatory=>true, :default=>codons_stop, :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=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'} options = Biopieces.options_parse(ARGV, casts) -- 2.39.5