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Revision 1.2 - (download) (as text) (annotate)
Tue Feb 20 21:02:02 2007 UTC (13 years, 1 month 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: +2 -2 lines
changed ; to :: for key separator

$genome = shift(@ARGV);
opendir(DIR,"/vol/seed-attributes/computation_results/SignalP");
open(OUT,">/vol/seed-attributes/SignalP/SignalP_attributes_for_$genome.txt");
@files = readdir(DIR);
foreach $file (@files){
    if($file =~/($genome.peg.\d+).SignalP_result/){
	my $peg = $1;
	$peg = "fig|".$peg;
	my $string;
	my $record = 0;
	open(IN,"/vol/seed-attributes/computation_results/SignalP/$file");
	while($_ = <IN>){
	    chomp($_);
	    if ($_ =~/Prediction:\sSignal\speptide/){
		$string = "$peg\tSignalP::signal_peptide\t";
		$record = 1;
	    }
	    if ($_ =~/Signal peptide probability:(.*)/){
		if($record){
		    $probability = $1;
		    $string = $string.$1;
		    print OUT "$string\n";
		    $record = 0;
		}
	    }
	    if ($_ =~/Max cleavage site probability:\s(.*)\sbetween\spos.\s(.*)\sand\s(.*)$/){
		$score = $1;
		$location = $2."-".$3;
		if($score == 0.000){
		    #print "$peg\tSignalP_3.0_cleavage\tNo cleavage site 0.000\n";
		}
		else{
		    print OUT "$peg\tSignalP::cleavage_site\t$score;$location\n";
		}
	    }
	}
    }
}

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