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Revision 1.1 - (download) (as text) (annotate)
Sat Aug 26 21:10:13 2006 UTC (13 years, 5 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 add_to_subsystems

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

use strict;
use FIG;
my $fig = new FIG;

my $usage = "usage: add_to_subsystems 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`;

my($i);
foreach my $subsys (grep { $fig->usable_subsystem($_) } $fig->all_subsystems)
{
    if ($fig->ok_to_auto_update_subsys($subsys))
    {
	my @roles      = $fig->subsystem_to_roles($subsys);
	my @in_genomes = map { $_->[0] } @{$fig->subsystem_genomes($subsys,1)};
	my @possible = ();

	for ($i=0; ($i < @in_genomes) && ($in_genomes[$i] ne $genome); $i++) {}
	if ($i == @in_genomes)
	{
	    my $subsystem = $fig->get_subsystem($subsys);
	    my @genomes = grep { $genomes{$_} } @in_genomes;
	    if (@genomes > 0)
	    {
		foreach my $genome1 (@in_genomes)
		{
		    my $variant   = $subsystem->get_variant_code_for_genome($genome1);
		    if ($variant > 0)
		    {
			my @pegs_in_new = ();
			my $missed = 0;
			my $extra = 0;

			foreach my $role (@roles)
			{
			    if (! $missed)
			    {
				my @pegs = $fig->pegs_in_subsystem_cell($subsys,$genome1,$role);
				my @pegs1 = $fig->seqs_with_role($role,'master',$genome);
				push(@pegs_in_new,[@pegs1]);
				
				if ((@pegs1 == 0) && (@pegs > 0))
				{
				    $missed = 1;
				}
				elsif ((@pegs1 > 0) && (@pegs == 0))
				{
				    $extra++;
				}
			    }
			}

			if (! $missed)
			{
			    push(@possible,[$genome1,[@pegs_in_new],$extra,$variant]);
			}
		    }
		}
	    }
	}

	if (@possible > 0)
	{
	    @possible = sort { $a->[2] <=> $b->[2] } @possible;
	    &add_genome_to_subsystem($fig,\@roles,$subsys,$genome,$possible[0]->[3],$possible[0]->[1]);
	}
    }
}

sub add_genome_to_subsystem {
    my($fig,$roles,$subsys,$genome,$variant,$peg_sets) = @_;
    
    my $subsystem = $fig->get_subsystem($subsys);
    $subsystem->add_genome($genome);
    print STDERR "add $genome to $subsys, variant=$variant\n";
    my $idx = $subsystem->get_genome_index($genome);
    $subsystem->set_variant_code($idx,$variant);
    for (my $i=0; ($i < @$roles); $i++)
    {
	if (@{$peg_sets->[$i]} > 0)
	{
	    print STDERR "    ",join(",",(@{$peg_sets->[$i]})), " implement $roles->[$i]\n";
	}
	$subsystem->set_pegs_in_cell($genome,$roles->[$i],$peg_sets->[$i]);
    }
    $subsystem->write_subsystem;
}

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