[Bio] View of /FortyEight/rp_make_PSORT

Revision 1.3 - (download) (as text) (annotate)
Tue Jul 15 17:48:37 2008 UTC (11 years, 5 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, 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, 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 1.2: +1 -0 lines

handles possible multilocation pegs

my $jobdir = shift(@ARGV);
my $genome = shift(@ARGV);
my $date = localtime();

if(! -d "$jobdir/rp/$genome/attributes"){
    `mkdir $jobdir/rp/$genome/attributes`;
}

if(-e "$jobdir/rp/$genome/attributes/phenotypes.txt"){

    
    my $stain;
    open(IN,"$jobdir/rp/$genome/attributes/phenotypes.txt");
    while($_ = <IN>){
	if($_ =~/Gram_Stain\tPositive/){$stain = "Positive";}
	elsif($_ =~/Gram_Stain\tNegative/){$stain = "Negative";}
    }
    close(IN);

    print "$stain\n";

    my $score_threshold;
    if($stain =~/(Negative|Positive)/){
        if($stain eq "Negative"){$score_threshold = 2;}
        else{$score_threshold = 2.5;}
        $results = "/vol/seed-attributes/computation_results/Psort/$genome/$genome.output";
        open(IN,$results);
        my $peg;
        my $record = 0;
	open(OUT,">$jobdir/rp/$genome/attributes/psort.txt");
        while ($_ = <IN>){
            chomp($_);
            if($record){
                if($_ =~/(\w+)\s+(\d+.\d+)/){print OUT "$peg\tPSORT::$1\t$2\n";}
		elsif($_ =~/(\w+)\s+.*multiple.*(\d+.\d+)/){print OUT "$peg\tPSORT::$1\t$2\n";}
                elsif($_ =~/Unknown/){print OUT "$peg\tPSORT::unknown\tunknown\n";}
                $record = 0;
            }
            else{
                if($_ =~/(fig\|\d+.\d+.peg.\d+)/){$peg = $1;}
                if($_ =~/(CytoplasmicMembrane)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}}
                if($_ =~/(Cytoplasmic)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}}
                if($_ =~/(OuterMembrane)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}}
                if($_ =~/(Periplasmic)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}}
                if($_ =~/(Extracellular)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}}
                if($_ =~/(Cellwall)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}}
            }
            if($_ =~/Final Prediction/){$record = 1}
        }
	close(OUT);
    }
}

View of /FortyEight/rp_make_PSORT_attributes.pl