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

Diff of /FigKernelScripts/similar_to.pl

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

revision 1.1, Mon May 31 23:03:40 2004 UTC revision 1.4, Mon Dec 5 18:56:38 2005 UTC
# Line 1  Line 1 
1    #
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  use FIG;  use FIG;
19  my $fig = new FIG;  my $fig = new FIG;
20    
21  use Sim;  use Sim;
22    
23  my $usage = "usage: bbhs [CutOff] < PEG > PEG1-Sc-PEG";  my $usage = "usage: similar_to [CutOff] < PEG > PEG1-Sc-PEG";
24    
25  my($cutoff,$pair,$peg);  my($cutoff,$pair,$peg);
26  $cutoff = shift @ARGV;  $cutoff = shift @ARGV;
# Line 29  Line 46 
46                }                }
47              } <STDIN>;              } <STDIN>;
48    
49  %pegs = map { $_ => 1 } @pegs;  foreach $peg (@pegs)
   
 foreach $peg (keys(%pegs))  
50  {  {
51        if (! $seen{$peg})
52        {
53            $seen{$peg} = 1;
54      foreach $sim ($fig->sims($peg,1000,$cutoff,"fig"))      foreach $sim ($fig->sims($peg,1000,$cutoff,"fig"))
55      {      {
56          push(@hits,[$peg,$sim->psc,$sim->id2]);          push(@hits,[$peg,$sim->psc,$sim->id2]);
57                my $sc = $sim->psc;
58                my $id2 = $sim->id2;
59                print STDERR "$peg\t$sc\t$id2\n";
60            }
61      }      }
62  }  }
63    

Legend:
Removed from v.1.1  
changed lines
  Added in v.1.4

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3