[Bio] / FigKernelScripts / find_neighbors_using_figfams.pl Repository:
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revision 1.5, Wed Jan 30 22:50:37 2008 UTC revision 1.6, Thu Jan 31 15:31:39 2008 UTC
# Line 23  Line 23 
23  my $fig = new FIG;  my $fig = new FIG;
24    
25  use FigFams;  use FigFams;
 my $figfams = new FigFams($fig);  
   
 print STDERR "$0 using figfams in $figfams->{dir}\n";  
   
26  use ToCall;  use ToCall;
27  use NewGenome;  use NewGenome;
28    
# Line 42  Line 38 
38  my ($i, $fam_data, $to_call_dir, $N, $foundF);  my ($i, $fam_data, $to_call_dir, $N, $foundF);
39    
40  # First, let's determine which FigfamsData directory to use  # First, let's determine which FigfamsData directory to use
41  $fam_data = "$FIG_Config::data/FigfamsData";  
42  for ($i=0; ($i < @ARGV) && ($ARGV[$i] !~ /^-fams=/); $i++) {}  for ($i=0; ($i < @ARGV) && ($ARGV[$i] !~ /^-fams=/); $i++) {}
43  if ($i < @ARGV) {  if ($i < @ARGV) {
44      if ($ARGV[$i] =~ /^-fams=(\S+)/) {      if ($ARGV[$i] =~ /^-fams=(\S+)/) {
# Line 56  Line 52 
52      }      }
53  }  }
54    
55    my $figfams = new FigFams($fig, $fam_data);
56    
57  # Now pick up the normal parameters  # Now pick up the normal parameters
58  (  (
59   ($to_call_dir = shift @ARGV) &&   ($to_call_dir = shift @ARGV) &&

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