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Revision 1.4 - (download) (as text) (annotate)
Wed Oct 12 21:09:52 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.3: +1 -1 lines
Corrected usgae msg. -- /gdp

# -*- perl -*-

use FIG;
my $fig = new FIG;

my $usage   = "usage: check_starts_for_pegs [-v(erbose)] < list_of_FIDs > list_of_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,$objects) = $fig->call_start(&FIG::genome_of($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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