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

Diff of /FigKernelScripts/predict_starts.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.4, Sun Jul 24 15:54:40 2005 UTC revision 1.8, Fri Nov 30 21:53:05 2007 UTC
# Line 1  Line 1 
1    # -*- perl -*-
2    ########################################################################
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    
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) &&
# Line 11  Line 37 
37  )  )
38      || die $usage;      || die $usage;
39    
40  &FIG::run("make_calls_for_start_predictions < $objects > /tmp/with.calls.$$");  &FIG::run("make_calls_for_start_predictions < $objects > $FIG_Config::temp/with.calls.$$");
41  &FIG::run("order_corrections_for_start_predictions < /tmp/with.calls.$$ 2> /tmp/clear$$ > /tmp/proposed$$");  &FIG::run("order_corrections_for_start_predictions < $FIG_Config::temp/with.calls.$$ 2> $FIG_Config::temp/clear$$ > $FIG_Config::temp/proposed$$");
42  system "cat /tmp/clear$$ >> $clear_calls";  system "cat $FIG_Config::temp/clear$$ >> $clear_calls";
43  system "cat /tmp/proposed$$ >> $proposed";  system "cat $FIG_Config::temp/proposed$$ >> $proposed";
44  system "cat /tmp/with.calls.$$";  system "cat $FIG_Config::temp/with.calls.$$";
45  unlink("/tmp/with.calls.$$","/tmp/clear$$","/tmp/proposed$$");  unlink("$FIG_Config::temp/with.calls.$$","$FIG_Config::temp/clear$$","$FIG_Config::temp/proposed$$");
46    
47    

Legend:
Removed from v.1.4  
changed lines
  Added in v.1.8

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3