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Annotation of /FortyEight/rp_make_PHOBIUS_attributes.pl

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1 : mkubal 1.1 my $jobdir = shift(@ARGV);
2 :     my $genome = shift(@ARGV);
3 :     my $date = localtime();
4 :    
5 :     opendir(DIR,$jobdir."/$genome");
6 :     open(PHOB,">$jobdir/rp/$genome/PHOBIUS_attributes_for_$genome.txt");
7 :    
8 :     my @files = readdir(DIR);
9 :    
10 :     print PHOB "$genome\tPhobius_run_on_remote_server\t$date\n";
11 :     foreach my $file (@files){
12 :     if ($file =~/($genome.peg.\d+).PHOBIUS_result/){
13 :     my $peg = "fig|".$1;
14 :     open(IN,$jobdir."/$genome/$file");
15 :     my @tm_locations = ();
16 :     while ($_ = <IN>){
17 :     if($_ =~/SIGNAL\s+(\d+)\s+(\d+)/){
18 :     print PHOB "$peg\tPhobius::signal\t$1-$2\n";
19 :     }
20 :     if($_ =~/TRANSMEM\s+(\d+)\s+(\d+)/){
21 :     my $loc = "$1-$2";
22 :     push(@tm_locations,$loc);
23 :     }
24 :     }
25 :     close(IN);
26 :     if(scalar(@tm_locations) > 0){
27 :     my $loc_string = join(",",@tm_locations);
28 :     print PHOB "$peg\tPhobius::transmembrane\t$loc_string\n";
29 :     }
30 :     }
31 :     }
32 :    
33 :     close(PHOB);
34 :    
35 :     `rm $jobdir/$genome/*.PHOBIUS_result`;

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