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Revision 1.1 - (download) (as text) (annotate)
Fri May 2 16:56:48 2008 UTC (11 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, 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, 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
for new RAST genomes

use FIGV;

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

my $fig = new FIGV("$jobdir/rp/$genome");

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);

    if($stain){
	$results_dir = "/vol/seed-attributes/computation_results/Psort/$genome";
	
	if(! -d $results_dir){
	    `mkdir $results_dir`;
	}
	
	my $input_file = "$results_dir/$genome.fasta";
	my $output_file = "$results_dir/$genome.output";
	open(OUT,">$input_file");
	
	my @pegs = $fig->pegs_of($genome);
	foreach my $peg (@pegs){
	    if($peg =~/(\d+.\d+.peg.\d+)/){
		my $seq = $fig->get_translation($peg);
		print OUT ">$peg\n";
		print OUT "$seq\n";
	    }
	}
	close(OUT);
	
	open(QSUB,">$jobdir/rp/$genome/psort_job_$genome.sh");
	print QSUB "#!/usr/bin/sh\n";
	print QSUB "PATH=/home/mkubal/public_html/FIGdisk/env/cee/bin\n";

	if($stain eq "Positive"){
	    print QSUB "/vol/cee-2008-0403/linux-ppc/bin/psort -p $input_file > $output_file;\n";
	}
	else{
	    print QSUB "/vol/cee-2008-0403/linux-ppc/bin/psort -n $input_file > $output_file;\n";
	}
	close(QSUB);
	`qsub -q all.q $jobdir/rp/$genome/psort_job_$genome.sh`;
    }
}


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