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Annotation of /FigKernelScripts/make_Phobius_attributes.pl

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1 : mkubal 1.1 $genome = shift(@ARGV);
2 : mkubal 1.2 #for version enter date Phobius was run in format of mmddyy
3 :     $version = shift(@ARGV);
4 : mkubal 1.1 open(PHOB,">/vol/seed-attributes/Phobius/Phobius_attributes_for_$genome.txt");
5 :     opendir(DIR,"/vol/seed-attributes/computation_results/Phobius/$genome");
6 :     my @files = readdir(DIR);
7 :    
8 : mkubal 1.2 print PHOB "$genome\t$Phobius_run_on_remote_server\t$version\n";
9 : mkubal 1.1 foreach my $file (@files){
10 :     if ($file =~/($genome.peg.\d+).Phobius_result/){
11 :     my $peg = "fig|".$1;
12 :     open(IN,"/vol/seed-attributes/computation_results/Phobius/$genome/$file");
13 :     my @tm_locations = ();
14 :     while ($_ = <IN>){
15 :     if($_ =~/SIGNAL\s+(\d+)\s+(\d+)/){
16 :     print PHOB "$peg\tPhobius::signal\t$1-$2\n";
17 :     }
18 :     if($_ =~/TRANSMEM\s+(\d+)\s+(\d+)/){
19 :     my $loc = "$1-$2";
20 :     push(@tm_locations,$loc);
21 :     }
22 :     }
23 :     close(IN);
24 :     if(scalar(@tm_locations) > 0){
25 :     my $loc_string = join(",",@tm_locations);
26 :     print PHOB "$peg\tPhobius::transmembrane\t$loc_string\n";
27 :     }
28 :     }
29 :     }
30 :    
31 :    
32 : mkubal 1.2

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