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Revision 1.7 - (download) (as text) (annotate)
Mon Dec 18 01:21:56 2006 UTC (12 years, 11 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 1.6: +1 -1 lines
fix call to rapid_subsystem_extension in check_and_extend_all_subsystems

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

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

use strict;

# usage: check_and_extend_all_subsyst [-i] [-norebuild]     # use -i to actually install';
#                                                           # use -norebuild to suppress recomputing 
#                                                           # Subsystem directories;

my $install = 0;
my $rebuild = 1;

foreach my $arg (@ARGV)
{
    if      ($arg eq "-i")        { $install = 1 }
    elsif   ($arg = "-norebuild") { $rebuild = 0 }
}
if ($install) { print STDERR "this run will install additions to extendable genomes\n" }
if ($rebuild) { print STDERR "this run will rebuild the Subsystems directories\n" }

my $has = &build_current_subsystem_data($fig,$rebuild);
&what_needs_to_be_done($fig,$has,$install);

sub build_current_subsystem_data {
    my($fig,$rebuild) = @_;

    my($genome);
    my $has = {};
    foreach $genome (sort { $a <=> $b } $fig->genomes('complete'))
    {
	my $tmpF = "$FIG_Config::organisms/$genome/Subsystems";
	if ((-d $tmpF) && $rebuild)
	{
	    system "rm -rf $tmpF";
	}
	if ($rebuild || (! -d $tmpF))
	{
	    system "rapid_subsystem_inference  $tmpF < $FIG_Config::organisms/$genome/assigned_functions";
	    print STDERR "Finished updating Subsystems for $genome\n";
	}

	if (open(SUBS,"<$tmpF/subsystems"))
	{
	    while (defined($_ = <SUBS>))
	    {
		if ($_ =~ /^([^\t]+)\t(\S+)/)
		{
		    $has->{$1}->{$genome} = "\*$2";
		}
	    }
	    close(SUBS);
	}
    }
    return $has;
}

sub what_needs_to_be_done {
    my($fig,$has,$install) = @_;

    foreach my $sub (grep { $fig->ok_to_auto_update_subsys($_) } $fig->all_subsystems)
    {
	my $altered = 0;
	if (my $hasH = $has->{$sub})
	{
	    my $subsys = new Subsystem($sub,$fig);
	    my %genomes_in = map { $_ => 1 } $subsys->get_genomes;
	    foreach my $genome (grep { (! $genomes_in{$_}) && $fig->is_prokaryotic($_) } sort { $a <=> $b } keys(%$hasH))
	    {
		my $curator = $subsys->get_curator;
		my $var     = $hasH->{$genome};
		print STDERR join("\t",($sub,$curator,$genome,$var,$fig->genus_species($genome))),"\n";
		if ($install && open(BINDINGS,"<$FIG_Config::organisms/$genome/Subsystems/bindings"))
		{
		    my %by_role;
		    while (defined($_ = <BINDINGS>))
		    {
			chop;
			my($sub_name,$role,$peg) = split(/\t/,$_);
			if ($sub_name eq $sub)
			{
			    push(@{$by_role{$role}},$peg);
			}
		    }
		    close(BINDINGS);
		    
		    $subsys->add_genome($genome);
		    $altered = 1;
                    $subsys->set_variant_code($subsys->get_genome_index($genome),$var);
		    foreach my $role ($subsys->get_roles)
		    {
			if (my $pegs = $by_role{$role})
			{
			    $subsys->set_pegs_in_cell($genome,$role,$pegs);
			}
		    }
		}
	    }

	    if ($install && $altered)
	    {
		$subsys->write_subsystem;
	    }
	}
    }
}
			

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