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Revision 1.1 - (download) (as text) (annotate)
Sat Aug 19 22:29:15 2006 UTC (13 years, 2 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
add potentially_missed_assignments

########################################################################
use strict;

use FIG;
my $fig = new FIG;

my $usage = "potentially_missed_assignments User GenomeToBeAnnotated FileOfGenomesGivingContext";

my($genome,$contextF,$user,%proposed);
(
 ($user     = shift @ARGV) &&
 ($genome   = shift @ARGV) &&
 ($contextF = shift @ARGV) && (-s $contextF)
)
    || die $usage;

$user =~ s/^master://;

my %genomes = map { $_ =~ /^(\S+)/; $1 => 1 } `cat $contextF`;
foreach my $subsys (grep { $fig->usable_subsystem($_) } $fig->all_subsystems)
{
    my @roles    = $fig->subsystem_to_roles($subsys);
    my @genomes  = map { $_->[0] } grep { $genomes{$_->[0]} } @{$fig->subsystem_genomes($subsys,0)};
    if (@genomes > 0)
    {
        foreach my $role (@roles)
        {
            foreach my $genome1 (@genomes)
            {
                my @pegs = $fig->pegs_in_subsystem_cell($subsys,$genome1,$role);
                foreach my $peg (@pegs)
		{
		    my $needed_func = $fig->function_of($peg);
		    my @bbhs = grep { &FIG::genome_of($_) eq $genome } map { $_->[0] } $fig->bbhs($peg,1.0e-50);
		    if (@bbhs == 1)
		    {
			my $candidate = $bbhs[0];
			if ((! $proposed{$candidate}) && ($needed_func ne scalar $fig->function_of($candidate)))
			{
			    if ($fig->auto_assign($candidate) eq $needed_func)
			    {
				$proposed{$candidate} = $needed_func;
			    }
			}
		    }
		}
	    }
	}
    }
}

my @proposed = map { [$_,$proposed{$_}] } keys(%proposed);
if (@proposed > 0)
{
    my $n = @proposed;
    print STDERR "Installing an assignment set for $user containing $n proposed assignments\n";
    open(ASSIGNMENTS,"| make_assignments_set $user subsystem_based new_genome")
	|| die "could not make new assignments set";
    foreach $_ (@proposed)
    {
	print ASSIGNMENTS join("\t",@$_),"\n";
    }
    close(ASSIGNMENTS);
}

		    
		

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