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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 : mkubal 1.2 #format for date is mmddyy
3 :     $date = shift(@ARGV);
4 :    
5 : mkubal 1.1 open(IN,"/vol/seed-attributes/computation_results/Pfam_TimeLogic_HMM_Search/$genome");
6 :     open(PFAM,">/vol/seed-attributes/PFAM/PFAM_hmm_derived_attributes_for_$genome.txt");
7 :    
8 : mkubal 1.2 print PFAM "$genome\tPFAM_attribute_by_HMM_search_on_TimeLogic\t$date;Pfam_version_22\n";
9 :    
10 : mkubal 1.1 my $id;
11 :     my $pf;
12 :     my $start;
13 :     my $end;
14 :     my $evalue;
15 :     my $score;
16 :    
17 :     while ($_ = <IN>){
18 :     if($_ =~/(fig\|\d+.\d.peg.\d+)/){
19 :     $id = $1;
20 :     }
21 :    
22 :     if($_ =~/^\sA\s=\s(PF\d+)/){
23 :     $pf = $1;
24 :     }
25 :    
26 :     if($_ =~/E_Value =\s+(.*)/){
27 :     $evalue = $1;
28 :     chomp($evalue);
29 :     }
30 :    
31 :     if($_ =~ /QS =\s+(\d+)\s+QE =\s+(\d+)/){
32 :     $start = $1;
33 :     $end = $2;
34 :     if($evalue =~/(\d+)e-(\d+)/){
35 :     $part1 = $1;
36 :     $part2 = $2;
37 :     if($part2 > 19){
38 :     $part2 = (1000 - $part2);
39 :     $part1 = $part1 * 100;
40 :     $score = $part2.".".$part1;
41 :     print PFAM "$id\tPFAM::$pf\t$score;$start-$end\n";
42 :     }
43 :     }
44 :     if($evalue eq "0"){
45 :     print PFAM "$id\tPFAM::$pf\t0.0;$start-$end\n";
46 :     }
47 :     }
48 :     }
49 :     close(IN);
50 :    

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