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Revision 1.3 - (download) (as text) (annotate)
Wed Oct 17 15:31:41 2007 UTC (12 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, 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 1.2: +1 -1 lines
writes/reads to /rp/genome

use LWP;
use URI;
use FIGV;

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

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

my @pegs = $fig->pegs_of($genome);
foreach my $peg (@pegs){
    $seq = $fig->get_translation($peg);
    if($peg =~/(\d+.\d+.peg.\d+)/){$peg = $1;}
    $file = $jobdir."/rp/$genome/$peg".".CELLO_result";
    open(OUT,">$file");
    
    #CELLO
    print OUT "\nXXXCELLOXXX\n";
    #temp Hack for JGI genonme
    my $species = "gramp";
#    if($gram eq "positive"){
#	$species = "gramp";
#    }
#    else{
#	$species = "pro";
#    }
    
    my $browser = LWP::UserAgent->new;
    $url = "http://cello.life.nctu.edu.tw/cgi/main.cgi";
    my $response = $browser->post($url,
				  [
				   'species' => $species,
				   'file' => " ",
				   'seqtype' => "prot",
				   'fasta' => $seq,
				       'Submit' => "Submit",
				   ]
				  );
    
    print OUT $response->content;
    close(OUT);
}


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