[Bio] / FigKernelScripts / process_one_exp_dir.pl Repository:
ViewVC logotype

View of /FigKernelScripts/process_one_exp_dir.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (download) (as text) (annotate)
Tue Apr 19 20:23:43 2011 UTC (8 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, rast_rel_2011_0928, mgrast_dev_10262011, HEAD
Changes since 1.3: +1 -1 lines
fix typo

use Data::Dumper;
use strict;
use ExpressionDir;
use FIG;

@ARGV == 5 or die "Usage: $0 genome-id probes CDF experiments expr-dir\n";

my $genome_id = shift;
my $probes = shift;
my $cdf = shift;
my $experiments = shift;
my $expr_dir = shift;

my $fig = new FIG;

if (! -d "$FIG_Config::organisms/$genome_id")
{
    my $pdir = "/vol/pseed/FIGdisk/FIG/Data/Organisms/$genome_id";

    if (-d $pdir)
    {
	$fig = FIGV->new($pdir);
    }
}
    
my $e = ExpressionDir->create($expr_dir, $genome_id, $fig);

if ($probes =~ /\.sif$/)
{
    $e->compute_rma_normalized_from_sif($cdf, $probes, $experiments);
}
elsif ($probes =~ /\.tags$/)
{
    $e->compute_rma_normalized_from_locus_tags($cdf, $probes, $experiments);
}
elsif ($probes =~ /\.corr$/)
{
    $e->compute_rma_normalized_from_pegidcorr($cdf, $probes, $experiments);
}
else
{
    $e->compute_probe_to_peg($probes);
    
    $e->compute_rma_normalized($cdf, $experiments);
}

$e->compute_atomic_regulons();

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3