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Revision 1.2 - (download) (as text) (annotate)
Wed Feb 21 16:50:06 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: +9 -2 lines
test for dir exist

use LWP;
use URI;
use FIG;

#enter SEED genome id as first argument
$genome = shift(@ARGV);

#enter either positive or negative as 2nd argument
$gram = shift(@ARGV);

$fig = new FIG;

$dir = "/vol/seed-attributes/computation_results/CELLO_and_TMPRED/$genome";

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

@pegs = $fig->pegs_of($genome);
foreach $peg (@pegs){
    $seq = $fig->get_translation($peg);
    if($peg =~/(\d+.\d+.peg.\d+)/){$peg = $1;}
    $file = "/vol/seed-attributes/computation_results/CELLO_and_TMPRED/$genome/$peg".".CELLO_and_TMPRED_result";
    open(OUT,">$file");
    
    #TMPRED

    print OUT "\nXXXTMPREDXXX\n";
    my $browser = LWP::UserAgent->new;
    $url = "http://www.ch.embnet.org/cgi-bin/TMPRED_form_parser";
    my $response = $browser->post($url,
				  [
				   'outmode' => "html",
				   'min' => "17",
				   'max' => "33",
				   'comm' => "FIGSEQ",
				   'format' => "plain_text",
				   'seq' => $seq
				   ]
				  );
    
    print OUT $response->content;
    
    #CELLO
    print OUT "\nXXXCELLOXXX\n";
    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);
    #exit;
}


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