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Revision 1.1 - (download) (as text) (annotate)
Tue Jan 15 21:44:06 2008 UTC (11 years, 10 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, 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
fasta file as input

use LWP;
use URI;

$file = shift(@ARGV);

open(IN,$file);
%id_to_seq;
my $id;
my $seq;
while($_ = <IN>){
    chomp($_);
    if($_ =~/^>(.*)/){
	if($id){$id_to_seq{$id} = $seq;}
	$id = $1;
	$seq = "";
    }
    else{
	if($_=~/\w/){
	    $seq .= $_;
	}
    }
}
$id_to_seq{$id} = $seq;

close(IN);

my $counter = 0;
foreach my $id (keys(%id_to_seq)){
    print "$id\n";
    $seq = $id_to_seq{$id};
    $counter++;
    $file = "$counter".".Phobius_result";
    open(OUT,">$file");
    
    my $browser = LWP::UserAgent->new;
    $url = "http://phobius.sbc.su.se/cgi-bin/predict.pl ";
    my $response = $browser->post($url,
				  [
				   'protseq' => "$seq",
				   'format' => "nog",
				   'Submit' => "Submit"
				   ]
				  );
    
    print OUT $response->content;
    close(OUT);
    sleep(1);
}


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