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Revision 1.3 - (download) (as text) (annotate)
Tue Oct 23 16:51:29 2007 UTC (12 years, 5 months ago) by mkubal
Branch: MAIN
CVS Tags: rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_2008_0924, rast_rel_2008_04_23, rast_rel_2008_09_30, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, mgrast_rel_2008_0625, rast_rel_2008_10_09, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, mgrast_rel_2008_1110, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, rast_rel_2008_08_07
Changes since 1.2: +2 -1 lines
error checking

#  _*_ Perl _*_
#
# 
#

use strict;
use FIGV;


my ($genome_id,$orgdir) = @ARGV;

my $fig;
if($orgdir)
{
    $fig = new FIGV($orgdir);
}
else
{
    $fig = new FIGV;
}

chomp $genome_id;

unless (defined $genome_id)
{
    print STDERR "\nusage: run_flux_optimization <genome_id>\n";
    exit -1;
}

my $filebase = $fig->model_directory($genome_id)."/Analysis/";
print STDERR "FO:$filebase\n";
my %outputs;
open(OUTPUTS,$filebase."outputs.txt") or
    die("Failed to open $filebase\.outputs.txt");
while(<OUTPUTS>)
{
    my @tmp = split "\t" , $_;
    chomp @tmp;
    $outputs{$tmp[0]} = 1;
}
close(OUTPUTS);

system(("/vol/biotools/bin/glpsol","--max",$filebase.$genome_id.".mps","-o",$filebase."flux.output"));

#lets analyze the flux output
my $flux = 0;
my %sinks_used;
my %inputs_notused;
open(FLUX,$filebase."flux.output") 
    or die("Failed to open flux file ".$filebase."flux.output");
while(<FLUX>)
{
    if($_ =~ /^Objective/)
    {
	my @temp = split " ",$_;
	chomp @temp;
	if($temp[3] > 0)
	{
	    $flux = $temp[3];
	}
    }
    if($_ =~ /S(\d{5})/) #Sink rxn
    {
	my @temp = split " ",$_;
	chomp @temp;
	if($temp[3] != 0 && $outputs{"C".$1} != 1)
	{
	    $sinks_used{"C".$1} = $temp[3];
	}
    }
    if($_ =~ /U(\d{5})/) #Uptake rxn
    {
	my @temp = split " ",$_;
	chomp @temp;
	if($temp[3] == 0)
	{
	    $inputs_notused{"C".$1} = 1;
	}
    }
}
close(FLUX);

open(OUT,">".$filebase."flux_info.txt");

print OUT "Generated $flux biomass with compound uptake limit of 1000\n\n#######\n\n";
map { print OUT "Sink $_ excreted $sinks_used{$_}\n";} keys %sinks_used;
print OUT "\n#########\n\n";
map { print OUT "Input $_ not used\n";} keys %inputs_notused;

close(OUT);

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