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1 : overbeek 1.3 # -*- perl -*-
2 : olson 1.5 #
3 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 :     #
18 :    
19 : overbeek 1.3
20 : overbeek 1.1 use FIG;
21 :     my $fig = new FIG;
22 :    
23 : overbeek 1.4 my $usage = "usage: check_starts_for_pegs [-v(erbose)] < list_of_FIDs > list_of_old-new-conf-trans";
24 : overbeek 1.1 my $verbose = ((@ARGV > 0) && ($ARGV[0] =~ /-v/i));
25 :    
26 :     while (defined($_ = <STDIN>))
27 :     {
28 :     chomp;
29 :     @pegs = ($_ =~ /fig\|\d+\.\d+\.peg\.\d+/g);
30 :     if (@pegs > 0)
31 :     {
32 :     $peg = shift @pegs;
33 :     if (@pegs == 0)
34 :     {
35 :     @pegs = map { $_->id2 } $fig->sims($peg,20,1.0e-30,"fig");
36 :     }
37 :    
38 :     if (($loc = $fig->feature_location($peg)) && ($tran = $fig->get_translation($peg)))
39 :     {
40 : overbeek 1.2 ($recalled,$conf,$tranR,$proposed,$objects) = $fig->call_start(&FIG::genome_of($peg),$loc,$tran,\@pegs);
41 :     if ($recalled && ($recalled ne $loc))
42 :     {
43 :     print "$peg\t$loc\t$recalled\t$conf\t$tranR\n";
44 :     if ($verbose)
45 :     {
46 :     print STDERR "ID=$peg\n$proposed";
47 :     }
48 :     }
49 : overbeek 1.1 }
50 :     }
51 :     }
52 :    

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