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Revision 1.1 - (download) (as text) (annotate)
Sat Jun 15 16:35:53 2013 UTC (6 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2014_0729, rast_rel_2014_0912, HEAD
quality control using ribo proteins

use strict;
use Data::Dumper;
use FIG;
my $fig = new FIG;

my @genomes = grep { $fig->is_prokaryotic($_) } $fig->genomes('complete');

foreach my $g (@genomes)
{
    my $gs = $fig->genus_species($g);
    my $tax = $fig->taxonomy_of($g);
    if ((-s "$FIG_Config::organisms/$g/contigs" < 100000000) &&
	(-s "$FIG_Config::organisms/$g/contigs" > 100000) &&
	($tax !~ /(plasmid|phage|virus)/i))
    {
	print "$g\t$gs\n";
	print "$tax\n";
#	my @out = `perl compute_ribo_ratio.pl -Dir ../Data.4-29-2013 < $FIG_Config::organisms/$g/contigs`;
#	foreach $_ (@out) { print $_ }
#	print "-\n";
	my @out = `perl compute_ribo_ratio_by_function.pl -g $g < $FIG_Config::organisms/$g/contigs`;
	foreach $_ (@out) { print $_ }
	print "---\n";
    }
}


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