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Revision 1.1 - (download) (as text) (annotate)
Thu Aug 16 15:59:26 2007 UTC (12 years, 6 months ago) by mkubal
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
runs Phobius computation for given geneome

use LWP;
use URI;
use FIG;

#enter SEED genome id as first argument
#$genome = shift(@ARGV);

$fig = new FIG;
@cgs = $fig->genomes('complete');

foreach my $genome (@cgs){
    if($genome eq "83333.1"){next}
    if($fig->is_eukaryotic($genome)){next}

    $dir = "/vol/seed-attributes/computation_results/Phobius/$genome";

    if(-d $dir){
	$already_there = 1;
	next;
    }
    else{
	`mkdir /vol/seed-attributes/computation_results/Phobius/$genome`;
    }    
    
    @pegs = $fig->pegs_of($genome);
    foreach $peg (@pegs){
	print "$peg\n";
	$seq = $fig->get_translation($peg);
	if($peg =~/(\d+.\d+.peg.\d+)/){$peg = $1;}
	$file = "/vol/seed-attributes/computation_results/Phobius/$genome/$peg".".Phobius_result";
	open(OUT,">$file");
	
	my $browser = LWP::UserAgent->new;
	$url = "http://phobius.cgb.ki.se/cgi-bin/predict.pl ";
	my $response = $browser->post($url,
				      [
				       'protseq' => "$seq",
				       'format' => "nog",
				       'Submit' => "Submit"
				       ]
				      );
	
	print OUT $response->content;
	close(OUT);
	#print $response->content;
	sleep(1);
    }
    
}

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