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Annotation of /FortyEight/rp_CELLO_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 $fig = new FIGV("$jobdir/rp/$genome");
9 : mkubal 1.1
10 : mkubal 1.2 my @pegs = $fig->pegs_of($genome);
11 :     foreach my $peg (@pegs){
12 : mkubal 1.1 $seq = $fig->get_translation($peg);
13 :     if($peg =~/(\d+.\d+.peg.\d+)/){$peg = $1;}
14 : mkubal 1.3 $file = $jobdir."/rp/$genome/$peg".".CELLO_result";
15 : mkubal 1.1 open(OUT,">$file");
16 :    
17 :     #CELLO
18 :     print OUT "\nXXXCELLOXXX\n";
19 :     #temp Hack for JGI genonme
20 :     my $species = "gramp";
21 :     # if($gram eq "positive"){
22 :     # $species = "gramp";
23 :     # }
24 :     # else{
25 :     # $species = "pro";
26 :     # }
27 :    
28 :     my $browser = LWP::UserAgent->new;
29 :     $url = "http://cello.life.nctu.edu.tw/cgi/main.cgi";
30 :     my $response = $browser->post($url,
31 :     [
32 :     'species' => $species,
33 :     'file' => " ",
34 :     'seqtype' => "prot",
35 :     'fasta' => $seq,
36 :     'Submit' => "Submit",
37 :     ]
38 :     );
39 :    
40 :     print OUT $response->content;
41 :     close(OUT);
42 :     }
43 :    

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