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Revision 1.2 - (download) (as text) (annotate)
Wed Feb 21 16:55:43 2007 UTC (13 years 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: +7 -2 lines
test for dir exist

use FIG;
$fig = new FIG;

my $genome = shift(@ARGV);
my $gram = shift(@ARGV);
my %hash;
my $type;

if($genome !~/\d+.\d+/){print "must supply valid genome id\n"; exit;}

if($gram eq "negative"){$type = "gram-"}
elsif($gram eq "positive"){$type = "gram+"}
else{print "must supply gram type\n"; exit;}

$dir = "/vol/seed-attributes/computation_results/SignalP/$genome";
if(-d $dir){
    $already_there = 1 ;
}
else{
    `mkdir $dir`;
}     

open(FASTA,"$FIG_Config::organisms/$genome/Features/peg/fasta");
foreach $key (keys(%hash)){delete($hash{$key})};
my $peg;
my $seq;
while ($_ = <FASTA>){
    if($_ =~/(fig.*\d)/){
	if($peg){
	    $hash{$peg} = $seq;
	}
	$seq = "";
	$peg = $1;
    }
    else{
	$seq = $seq."$_";
    }
}

foreach $key (keys(%hash)){
    open(TEMP,">$FIG_Config::temp/SignalP_temp.txt");
    $seq = $hash{$key};
    $key =~s/fig\|//;
    print TEMP ">$key\n";
    print TEMP "$seq";
    close(TEMP);
    
    $input_file = "$FIG_Config::temp/SignalP_temp.txt";   
    `/vol/seed-attributes/bin/signalp-3.0/signalp -t $type $input_file > /vol/seed-attributes/computation_results/SignalP/$key.SignalP_result`;
}


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