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Revision 1.1 - (download) (as text) (annotate)
Thu Nov 30 23:04:16 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, 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, rast_rel_2008_04_23, 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
put in the fr2go stuff

########################################################################


# usage: update_fr2go 
#
# updates the Data/Ontologies/GO/fr2go file and reloads the GO dbs.

use FIG;
my $fig = new FIG;

open(FR2GO,"| sort -u > $FIG_Config::data/Ontologies/GO/fr2go")
    || die "$FIG_Config::data/Ontologies/GO/fr2go";

foreach $_ (`cat $FIG_Config::data/Ontologies/GO/ec2go`)
{
    if ($_ =~ /^EC:(\d+\.\d+\.\d+\.\d+)\s+>\s+.*(GO:\d{7})/)
    {
	push(@{$ec2go{$1}},$2);
    }
}

foreach $subsys (grep { $fig->usable_subsystem($_) } $fig->all_subsystems)
{
    @roles    = $fig->subsystem_to_roles($subsys);
    foreach $role (@roles)
    {
	@ecs = ($role =~ /\(EC \d+\.\d+\.\d+\.\d+\)/g);
	if (@ecs > 0)
	{
	    foreach $ec (@ecs)
	    {
		if (($ec =~ /^\(EC (\d+\.\d+\.\d+\.\d+)\)/) && ($x = $ec2go{$1}))
		{
		    foreach $go (@$x)
		    {
			$fr2go{$role}->{$go} = 1;
		    }
		}
	    }
	}
    }
}

foreach $role (keys(%fr2go))
{
    $x = $fr2go{$role};
    foreach $go (keys(%$x))
    {
	print STDERR "$role\t$go\n";
	print FR2GO "$role\t$go\n";
    }
}

open(PEG2GO,"<$FIG_Config::data/Ontologies/GO/peg2go")
    || die "where is peg2go?";
while (defined($_ = <PEG2GO>))
{
    if ($_ =~ /^(\S+)\t(\S+)/)
    {
	$peg = $1;
	$go  = $2;
	$func = $fig->function_of($peg);
	if (($func !~ / [\@\/] /) && ($func !~ /; /))
	{
	    my @tmp = $fig->peg_to_roles_in_subsystems($peg);
	    if (@tmp > 0)
	    {
		$role = $tmp[0]->[1];
		if (! $fr2go{$role})
		{
		    $fr_to_go_by_peg{$role}->{$go}++;
		}
	    }
	}
    }
}
close(PEG2GO);

foreach $role (keys(%fr_to_go_by_peg))
{
    $x = $fr_to_go_by_peg{$role};
    foreach $go (keys(%$x))
    {
	if ($x->{$go} > 1)
	{
	    print STDERR "$role\t$go\n";
	    print FR2GO "$role\t$go\n";
	}
    }
}
close(FR2GO);

system "$FIG_Config::bin/load_go";


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