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Annotation of /FigKernelScripts/check_starts_for_pegs.pl

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1 : overbeek 1.3 # -*- perl -*-
2 :    
3 : overbeek 1.1 use FIG;
4 :     my $fig = new FIG;
5 :    
6 : overbeek 1.4 my $usage = "usage: check_starts_for_pegs [-v(erbose)] < list_of_FIDs > list_of_old-new-conf-trans";
7 : overbeek 1.1 my $verbose = ((@ARGV > 0) && ($ARGV[0] =~ /-v/i));
8 :    
9 :     while (defined($_ = <STDIN>))
10 :     {
11 :     chomp;
12 :     @pegs = ($_ =~ /fig\|\d+\.\d+\.peg\.\d+/g);
13 :     if (@pegs > 0)
14 :     {
15 :     $peg = shift @pegs;
16 :     if (@pegs == 0)
17 :     {
18 :     @pegs = map { $_->id2 } $fig->sims($peg,20,1.0e-30,"fig");
19 :     }
20 :    
21 :     if (($loc = $fig->feature_location($peg)) && ($tran = $fig->get_translation($peg)))
22 :     {
23 : overbeek 1.2 ($recalled,$conf,$tranR,$proposed,$objects) = $fig->call_start(&FIG::genome_of($peg),$loc,$tran,\@pegs);
24 :     if ($recalled && ($recalled ne $loc))
25 :     {
26 :     print "$peg\t$loc\t$recalled\t$conf\t$tranR\n";
27 :     if ($verbose)
28 :     {
29 :     print STDERR "ID=$peg\n$proposed";
30 :     }
31 :     }
32 : overbeek 1.1 }
33 :     }
34 :     }
35 :    

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