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Revision 1.1 - (download) (as text) (annotate)
Wed Jun 18 15:49:10 2008 UTC (11 years, 8 months ago) by arodri7
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
update changes

use FIG;
my $fig = new FIG;

my $usage = "usage: PDB_to_FIGfams_worker FigfamsData OutDir ProcN";
my ($ff_data, $outD, $procN);
(
 ($ff_data = shift @ARGV) &&
 ($outD    = shift @ARGV) &&
 ($procN   = shift @ARGV)
)
    || die $usage;

use FFs;
my $ffs = new FFs($ff_data);
print STDERR "starting $procN\n";

open(OUT,">$outD/$procN") || die "could not open $outD/$procN";

while (defined($_ = <STDIN>))
{
    chomp;
    my($id,$seq) = split(/\t/,$_);
    print STDERR "$id\t$seq\n\n";
    my @sims = $fig->dsims($id,$seq,5000,0.1,$ff_data,"-e 1.0e-5");
    undef %best;
    foreach my $sim (@sims)
    {
	my $peg  = $sim->id2;
	my $nbsc = $sim->nbsc;
	my @fams = $ffs->families_containing_peg($peg);
	foreach my $fam (@fams)
	{
	    if ((! $best{$fam}) || ($best{$fam}->[1] < $nbsc))
	    {
		$best{$fam} = [$peg,$nbsc,$sim];
	    }
	}
    }

    foreach $fam (sort keys(%best))
    {
	my($peg,$nbsc,$sim) = @{$best{$fam}};
	print OUT join("\t",($fam,
			     $sim->id1,$sim->id2,$sim->iden,$sim->b1,$sim->e1,$sim->ln1,
			     $sim->b2,$sim->e2,$sim->ln2,$sim->psc,$sim->bsc,$sim->nbsc)),"\n";
    }
}
close(OUT);


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