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

Annotation of /FigKernelScripts/check_all_lost_sims.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (view) (download) (as text)

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 : efrank 1.1 $usage = "usage: check_all_lost_sims Deleted ReMapped OldSims NewSims";
19 :    
20 :     (($deleted = shift @ARGV) &&
21 :     ($remapped = shift @ARGV) &&
22 :     ($old = shift @ARGV) &&
23 :     ($new = shift @ARGV)
24 :     )
25 :     || die $usage;
26 :    
27 :     opendir(OLD,$old) || die "could not open $old";
28 :     @files = grep { $_ =~ /^\S/ } readdir(OLD);
29 :     closedir(OLD);
30 :    
31 :     foreach $file (@files)
32 :     {
33 :     $fileB = $file;
34 :     $fileB =~ s/\.gz$//;
35 :    
36 :     if ((-s "$old/$file") && (! -s "$new/$fileB"))
37 :     {
38 :     print "LOST FILE: $file\n";
39 :     }
40 :     if ($file eq $fileB)
41 :     {
42 :     system "check_lost_sims $deleted $remapped $new/$file < $old/$file";
43 :     }
44 :     else
45 :     {
46 :     system "zcat $old/$file | check_lost_sims $deleted $remapped $new/$file";
47 :     }
48 :     }

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3