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Revision 1.1 - (download) (as text) (annotate)
Sat Aug 20 02:37:22 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
fixes to call_starts

use FIG;
my $fig = new FIG;

my $usage   = "usage: check_starts_for_pegs [-v] > [old,new,conf,trans]";
my $verbose =  ((@ARGV > 0) && ($ARGV[0] =~ /-v/i));

while (defined($_ = <STDIN>))
{
    chomp;
    @pegs = ($_ =~ /fig\|\d+\.\d+\.peg\.\d+/g);
    if (@pegs > 0)
    {
	$peg = shift @pegs;
	if (@pegs == 0)
	{
	    @pegs = map { $_->id2 } $fig->sims($peg,20,1.0e-30,"fig");
	}

	if (($loc = $fig->feature_location($peg)) && ($tran = $fig->get_translation($peg)))
	{
	    ($recalled,$conf,$tranR,$proposed) = $fig->call_start(&FIG::genome_of($peg),$loc,$tran,\@pegs);
	    if ($recalled && ($recalled ne $loc))
	    {
		print "$peg\t$loc\t$recalled\t$conf\t$tranR\n";
		if ($verbose)
		{
		    print STDERR "ID=$peg\n$proposed";
		}
	    }
	}
    }
}
	

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