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Revision 1.2 - (download) (as text) (annotate)
Wed Aug 22 22:04:04 2007 UTC (12 years, 2 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
Changes since 1.1: +4 -0 lines
added date as 2nd argument

$genome = shift(@ARGV);
#for version enter date Phobius was run in format of mmddyy
$version = shift(@ARGV);
open(PHOB,">/vol/seed-attributes/Phobius/Phobius_attributes_for_$genome.txt");
opendir(DIR,"/vol/seed-attributes/computation_results/Phobius/$genome");
my @files = readdir(DIR);

print PHOB "$genome\t$Phobius_run_on_remote_server\t$version\n";
foreach my $file (@files){
    if ($file =~/($genome.peg.\d+).Phobius_result/){
	my $peg = "fig|".$1;
	open(IN,"/vol/seed-attributes/computation_results/Phobius/$genome/$file");
	my @tm_locations = ();
	while ($_ = <IN>){
	    if($_ =~/SIGNAL\s+(\d+)\s+(\d+)/){
		print PHOB "$peg\tPhobius::signal\t$1-$2\n";
	    }
	    if($_ =~/TRANSMEM\s+(\d+)\s+(\d+)/){
		my $loc = "$1-$2";
	        push(@tm_locations,$loc);
	    }
	}
	close(IN);
	if(scalar(@tm_locations) > 0){
	    my $loc_string = join(",",@tm_locations);
	    print PHOB "$peg\tPhobius::transmembrane\t$loc_string\n";
	}
    }
}




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