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Annotation of /FigKernelScripts/make_PFAM_HMM_derived_attributes.pl

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1 : mkubal 1.1 $genome = shift(@ARGV);
2 :     open(IN,"/vol/seed-attributes/computation_results/Pfam_TimeLogic_HMM_Search/$genome");
3 :     open(PFAM,">/vol/seed-attributes/PFAM/PFAM_hmm_derived_attributes_for_$genome.txt");
4 :    
5 :     my $id;
6 :     my $pf;
7 :     my $start;
8 :     my $end;
9 :     my $evalue;
10 :     my $score;
11 :    
12 :     while ($_ = <IN>){
13 :     if($_ =~/(fig\|\d+.\d.peg.\d+)/){
14 :     $id = $1;
15 :     }
16 :    
17 :     if($_ =~/^\sA\s=\s(PF\d+)/){
18 :     $pf = $1;
19 :     }
20 :    
21 :     if($_ =~/E_Value =\s+(.*)/){
22 :     $evalue = $1;
23 :     chomp($evalue);
24 :     }
25 :    
26 :     if($_ =~ /QS =\s+(\d+)\s+QE =\s+(\d+)/){
27 :     $start = $1;
28 :     $end = $2;
29 :     if($evalue =~/(\d+)e-(\d+)/){
30 :     $part1 = $1;
31 :     $part2 = $2;
32 :     if($part2 > 19){
33 :     $part2 = (1000 - $part2);
34 :     $part1 = $part1 * 100;
35 :     $score = $part2.".".$part1;
36 :     print PFAM "$id\tPFAM::$pf\t$score;$start-$end\n";
37 :     }
38 :     }
39 :     if($evalue eq "0"){
40 :     print PFAM "$id\tPFAM::$pf\t0.0;$start-$end\n";
41 :     }
42 :     }
43 :     }
44 :     close(IN);
45 :    

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