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revision 1.7, Mon Dec 5 18:56:38 2005 UTC revision 1.8, Fri Nov 30 21:53:05 2007 UTC
# Line 1  Line 1 
1  # -*- perl -*-  # -*- perl -*-
2  #  ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 14  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19    
20  use FIG;  use FIG;
21    use FIGV;
22  my $fig = new FIG;  my $fig = new FIG;
23    
24  $usage = "usage: predict_starts Objects ClearCalls ProposedCorrections";  $usage = "usage: predict_starts [-orgdir=OrgDir] Objects ClearCalls ProposedCorrections";
25    
26    $orgdir_flag = "";
27    if ($ARGV[0] =~ /-orgdir=(\S+)/) {
28        $fig = new FIGV($1);
29        $orgdir_flag = $ARGV[0];
30        shift @ARGV;
31    }
32    
33  (  (
34   ($objects       = shift @ARGV) &&   ($objects       = shift @ARGV) &&

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