[Bio] / FigKernelScripts / check_starts_for_peg_sets.pl Repository:
ViewVC logotype

Annotation of /FigKernelScripts/check_starts_for_peg_sets.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.5 - (view) (download) (as text)

1 : overbeek 1.4 # -*- 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 1.1
20 :     use FIG;
21 :    
22 :     $usage = "usage: check_starts_for_peg_sets ClearCorrections ProposedCorrections < sets > objects.with.calls";
23 :    
24 :     (
25 :     ($clear = shift @ARGV) &&
26 :     ($proposed = shift @ARGV)
27 :     )
28 :     || die $usage;
29 :    
30 :     while (defined($_ = <STDIN>))
31 :     {
32 :     chop;
33 :     @pegs = split(/\t/,$_);
34 :     if (@pegs > 2)
35 :     {
36 :     open(TMP,"| start_data_for_set_of_pegs use-close > tmp.objects$$")
37 :     || die "could not set up pipe to start_data_for_set_of_pegs";
38 :     foreach $peg (@pegs)
39 :     {
40 :     print TMP "$peg\n";
41 :     }
42 :     close(TMP);
43 : overbeek 1.2 &FIG::run("predict_starts tmp.objects$$ $clear $proposed > /dev/null");
44 : overbeek 1.1 }
45 :     }
46 :    
47 : overbeek 1.3 unlink("tmp.object$$");
48 : overbeek 1.1

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3