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1 : olson 1.2 #
2 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :     # for Interpretations of Genomes. All Rights Reserved.
4 :     #
5 :     # This file is part of the SEED Toolkit.
6 :     #
7 :     # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 :     # Public License.
10 :     #
11 :     # You should have received a copy of the SEED Toolkit Public License
12 :     # along with this program; if not write to the University of Chicago
13 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :     # Genomes at veronika@thefig.info or download a copy from
15 :     # http://www.theseed.org/LICENSE.TXT.
16 :     #
17 :    
18 : overbeek 1.1 use FIG;
19 :     my $fig = new FIG;
20 :    
21 :     my $usage = "usage: questionable_calls < PEGs > Func-ExtFunc-PEGs (with questionable calls)";
22 :    
23 :     @pegs = map { chop; $_ =~ /(\S+)$/;
24 :     $id = $1;
25 :     if ($id =~ /^fig\|/)
26 :     {
27 :     $id;
28 :     }
29 :     else
30 :     {
31 :     if ($peg = $fig->by_alias($id))
32 :     {
33 :     $peg;
34 :     }
35 :     else
36 :     {
37 :     ();
38 :     }
39 :     }
40 :     } <STDIN>;
41 :    
42 :     %pegs = map { $_ => 1 } @pegs;
43 :     @pegs = sort { &FIG::by_fig_id($a,$b) } keys(%pegs);
44 :    
45 :     foreach $pair ($fig->external_calls(\@pegs))
46 :     {
47 :     ($peg,$ext_func) = @$pair;
48 :     $ext_call{$peg} = $ext_func;
49 :     }
50 :    
51 :     foreach $peg (@pegs)
52 :     {
53 :     $func = $fig->function_of($peg);
54 :     if (! &FIG::hypo($func))
55 :     {
56 :     if (($ext = $ext_call{$peg}) && (! &FIG::hypo($ext)) && (! $fig->same_func($func,$ext)))
57 :     {
58 :     print "$func\t$ext\t$peg\n";
59 :     }
60 :     }
61 :     }
62 :    
63 :    
64 :    

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