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Revision 1.2 - (download) (as text) (annotate)
Tue Feb 20 21:03:15 2007 UTC (12 years, 9 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: +1 -1 lines
changed ; to :: for key separator

$genome = shift(@ARGV);
opendir(DIR,"/vol/seed-attributes/computation_results/CELLO_and_TMPRED/$genome");
open(TMPRED,">/vol/seed-attributes/TMPRED/TMPRED_attributes_for_$genome.txt");
open(CELLO,">/vol/seed-attributes/CELLO/CELLO_attributes_for_$genome.txt");

@files = readdir(DIR);
foreach $file (@files){
    if ($file =~/(\d+.\d+.peg.\d+).CELLO_and_TMPRED_result/){
	$peg = $1;
	open(IN,"/vol/seed-attributes/computation_results/CELLO_and_TMPRED/$genome/$file");
	$tmpred = 0;
	my $tmpred_score, $record_locations,@pairs,$pair,$location_string;
	while($_ = <IN>){
	    if(!$tmpred){
		if($_ =~/total score : (\d+)/){
		    $tmpred_score = $1;
		}
		if($record_locations){
		    if($_ =~/^\s\d+\s+(\d+)\s+(\d+)/){
			$pair = $1."-".$2;
			push(@pairs,$pair);
		    }
		    else{
			$tmpred = 1;
			$record_locations = 0;
			$location_string = join(",",@pairs);
			print TMPRED "fig|$peg\tTMPRED\t$tmpred_score;$location_string\n";
			@pairs = ();
		    }
		}
		if($_ =~/\sfrom\s+to\s+length\s+score\s+orientation/){
		    $record_locations = 1;
		}
	    }       
	    
	    if($_ =~/(Membrane|Extracellular|CellWall|Cytoplasmic|Periplasmic|InnerMembrane|OuterMembrane)\s?..td..td..nbsp..nbsp..nbsp..nbsp.(\d.\d+).nbsp..nbsp.\*/){
		$score = $2;
		if($1 =~/^Membrane/){$location = "membrane"}
		if($1 =~/Extracellular/){$location = "extracellular"}
		if($1 =~/CellWall/){$location = "cell wall"}
		if($1 =~/Cytoplasmic/){$location = "cytoplasm"}
		if($1 =~/OuterMembrane/){$location = "outer membrane"}
		if($1 =~/InnerMembrane/){$location = "inner membrane"}
		if($1 =~/Periplasmic/){$location = "periplasm"}
		
		print CELLO "fig|$peg\tCELLO::$location\t$score\n";
	    }
	}
    }
}

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