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Annotation of /FigKernelScripts/check_starts_for_pegs.pl

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1 : overbeek 1.1 use FIG;
2 :     my $fig = new FIG;
3 :    
4 :     my $usage = "usage: check_starts_for_pegs [-v] > [old,new,conf,trans]";
5 :     my $verbose = ((@ARGV > 0) && ($ARGV[0] =~ /-v/i));
6 :    
7 :     while (defined($_ = <STDIN>))
8 :     {
9 :     chomp;
10 :     @pegs = ($_ =~ /fig\|\d+\.\d+\.peg\.\d+/g);
11 :     if (@pegs > 0)
12 :     {
13 :     $peg = shift @pegs;
14 :     if (@pegs == 0)
15 :     {
16 :     @pegs = map { $_->id2 } $fig->sims($peg,20,1.0e-30,"fig");
17 :     }
18 :    
19 :     if (($loc = $fig->feature_location($peg)) && ($tran = $fig->get_translation($peg)))
20 :     {
21 : overbeek 1.2 ($recalled,$conf,$tranR,$proposed,$objects) = $fig->call_start(&FIG::genome_of($peg),$loc,$tran,\@pegs);
22 :     if ($recalled && ($recalled ne $loc))
23 :     {
24 :     print "$peg\t$loc\t$recalled\t$conf\t$tranR\n";
25 :     if ($verbose)
26 :     {
27 :     print STDERR "ID=$peg\n$proposed";
28 :     }
29 :     }
30 : overbeek 1.1 }
31 :     }
32 :     }
33 :    

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