[Bio] / FigKernelScripts / find_neighbors_using_figfams.pl Repository:
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revision 1.2, Fri Jun 1 04:19:16 2007 UTC revision 1.3, Fri Sep 14 18:10:21 2007 UTC
# Line 69  Line 69 
69  # we are doing) you would use ToCall.pm.  # we are doing) you would use ToCall.pm.
70    
71  my $to_call;  my $to_call;
72    my $old;
73    
74  if ((@ARGV > 0) && ($ARGV[0] =~ /^old/i)) {  if ((@ARGV > 0) && ($ARGV[0] =~ /^old/i)) {
75        $old = 1;
76      $to_call = new ToCall($to_call_dir);      $to_call = new ToCall($to_call_dir);
77  }  }
78  else {  else {
# Line 109  Line 112 
112              , " sims)\t$func\n"              , " sims)\t$func\n"
113              if $ENV{VERBOSE};              if $ENV{VERBOSE};
114    
115            my $fid;
116            if (! $old)
117            {
118          my $orf = &NewGenome::ORF::new('NewGenome::ORF', $to_call, $orf_id);          my $orf = &NewGenome::ORF::new('NewGenome::ORF', $to_call, $orf_id);
119          my $fid = $orf->promote_to_peg($sims, $func);              $fid = $orf->promote_to_peg($sims, $func);
120            }
121            else
122            {
123                $fid = $orf_id;
124            }
125    
126          if ($fid) {          if ($fid) {
127              push @peg_ids, $fid;              push @peg_ids, $fid;
128    

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