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Annotation of /FortyEight/rp_PHOBIUS_search.pl

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1 : mkubal 1.1 use LWP;
2 :     use URI;
3 :     use FIGV;
4 :    
5 :     my $jobdir = shift(@ARGV);
6 :     my $genome = shift(@ARGV);
7 :    
8 : mkubal 1.2 my $fig = new FIGV("$jobdir/rp/$genome");
9 : mkubal 1.1
10 :     my @pegs = $fig->pegs_of($genome);
11 :     foreach my $peg (@pegs){
12 :     my $seq = $fig->get_translation($peg);
13 :     if($peg =~/(\d+.\d+.peg.\d+)/){$peg = $1;}
14 : mkubal 1.3 my $file = $jobdir."/rp/$genome/$peg".".PHOBIUS_result";
15 : mkubal 1.1 open(OUT,">$file");
16 :     my $browser = LWP::UserAgent->new;
17 : mkubal 1.4 my $url = "http://phobius.sbc.su.se/cgi-bin/predict.pl";
18 : mkubal 1.1 my $response = $browser->post($url,
19 :     [
20 :     'protseq' => "$seq",
21 :     'format' => "nog",
22 :     'Submit' => "Submit"
23 :     ]
24 :     );
25 :     print OUT $response->content;
26 :     close(OUT);
27 :     sleep(1);
28 :     }

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