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Revision 1.2 - (download) (as text) (annotate)
Sat Oct 6 14:45:01 2007 UTC (12 years, 4 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
Changes since 1.1: +4 -3 lines
updates to computation of VCs

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

use FIG;
my $fig = new FIG;

$usage = "usage: run_find_subsys_against_all_genomes Subsystem Roles Definitions Rules > report";

(
 ($subsys    = shift @ARGV) &&
 ($rolesF    = shift @ARGV) &&
 ($defF      = shift @ARGV) &&
 ($rulesF    = shift @ARGV)
)
    || die $usage;

my $subO = new Subsystem($subsys,$fig);
my @genomes = $subO->get_genomes;
my @roles = $subO->get_roles;

foreach $genome (sort { $a <=> $b } @genomes)
{
    print "$genome\t",$fig->genus_species($genome),"\n";
    print STDERR "$genome\t",$fig->genus_species($genome),"\n";
    my(%by_role_sub,%by_role_tool,$role);
    foreach $role (@roles)
    {
	$by_role_sub{$role} = {};
	$by_role_tool{$role} = {};
    }

    my $vcS = $subO->get_variant_code_for_genome($genome);
    foreach $role (@roles)
    {
	my @pegs = $subO->get_pegs_from_cell($genome,$role);
	foreach $peg (@pegs)
	{
	    $by_role_sub{$role}->{$peg} = scalar $fig->function_of($peg);
	}
    }
    my $genomeD = "$FIG_Config::organisms/$genome";
    my @out = `find_subsys $subsys $rolesF $defF $rulesF $genomeD`;
    print STDERR join("",@out);

    my $x = shift @out; chop $x; ($x eq $subsys) || die "subsys should be $subsys";

    my $diff = 0;
    my $vcT = shift @out; chop $vcT;
    if ($vcT ne $vcS)
    {
	print "differing-VCs\texisting\t$vcS\tcomputed\t$vcT\n";
	$diff++;
    }
    while (($x = shift @out) && ($x !~ /^\/\//))
    {
	chop $x;
	my($role,$peg,$func) = split(/\t/,$x);
	$by_role_tool{$role}->{$peg} = $func;
    }

    foreach $role (sort keys(%by_role_sub))
    {
	$sH = $by_role_sub{$role};
	$tH = $by_role_tool{$role};

	my @pegsS = sort keys(%$sH);
	my @pegsT = sort keys(%$tH);
	my $i=0;
	my $j=0;
	while (($i < @pegsS) || ($j < @pegsT))
	{
	    if ($i == @pegsS)
	    {
		$diff++;
		print join("\t",("peg-in-tool-not-subsys",
				 $role,
				 $pegsT[$j],
				 $tH->{$pegsT[$j]}
				 )),"\n";
		$j++;
	    }
	    elsif ($j == @pegsT)
	    {
		$diff++;
		print join("\t",("peg-in-subsys-not-tool",
				 $role,
				 $pegsS[$i],
				 $sH->{$pegsS[$i]}
				 )),"\n";
		$i++;
	    }
	    else
	    {
		if ($sH->{$pegsS[$i]} ne $tH->{$pegsT[$j]})
		{
		    $diff++;
		    print join("\t",('mismatch-in-function',
				     $role,
				     $sH->{$pegsS[$i]},
				     $tH->{$pegsT[$j]}
				     )),"\n";
		}
		$i++;
		$j++;
	    }
	}
    }
    if (($vcT > 0) && ($diff == 0)) { print "$genome\t",$fig->genus_species($genome)," was perfect\n" }

    print "//\n";
}

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